programming python

Biopython nghe lén

Dự án Biopython là 1 tổ chức quốc tế của những lập trình viên sử dụng công cụ Python [http. //www. con trăn. org] trong lĩnh vực sinh học phân tử. Python là một ngôn ngữ lập trình hướng đối tượng, thông dịch, và linh hoạt nên đã trở nên phổ biến trong tính toán [computing] khoa học. Python dễ học, có cú pháp rõ ràng và có thể dễ dàng mở rộng với các module được viết bằng C, C++, hay FORTRAN

Website Biopython [biopython. org] có các tài nguyên online về các module, script, và web link cho các lập trình viên Python để sử dụng trong tin sinh học và nghiên cứu. Về cơ bản, mục tiêu của Biopython là làm cho việc sử dụng Python trong tin sinh học trở nên dễ dàng nhất có thể bằng cách tạo ra các module và lớp có thể tái sử dụng và có chất lượng cao. Biopython có các bộ chuyển đổi giữa các định dạng file dùng trong tin sinh học [BLAST, Clustalw, FASTA, Genbank,…], có kết nối với các service trực tuyến [NCBI, Expasy,…], giao diện với các phần mềm phổ biến cũng như hiếm dùng [Clustal, DSSP, MSMS,…], a standard sequence class, various clustering modules, a KD tree data structure,. v. v. và tài liệu

Về mặt cơ bản, chúng ta sẽ muốn lập trình bằng Python và làm nó trở nên dễ dàng nhất có thể để sử dụng Python trong tin sinh học bằng cách tạo ra các module và script có thể tái sử dụng và có chất lượng cao

2 Tôi có gì trong một gói Biopython?

Phiên bản Biopython chính có rất nhiều chức năng, bao gồm

– Khả năng chuyển đổi các file trong tin sinh học thành cấu trúc dữ liệu sử dụng trong Python, hỗ trợ các định dạng sau đây

+ Đầu ra của Blast – cả bản Blast độc lập lẫn bản web

+ Nghe lén

+ NHANH CHÓNG

+ Ngân hàng gen

+ PubMed và Medline

+ ExPASy file, chẳng hạn như Enzyme và Prosite

+ SCOP, bao gồm file ‘dom’ và ‘lin’

+ UniGene

+ SwissProt

– Những file thuộc định dạng được hỗ trợ có thể được lặp lại trong các bản ghi, hoặc sẽ được đánh chỉ số và được truy cập qua một giao diện Tra cứu [Dictionary]

– Mã để xử lý với những trạm xử lý tin sinh học online phổ biến như

+ NCBI – Blast, Entrez và PubMed services

+ ExPASy – các giá trị Swiss-Prot và Prosite cũng như tìm kiếm từ Prosite

– Giao diện với các chương trình tin sinh học thông dụng như

+ Bản Blast độc lập của NCBI

+ Chương trình alignment Clustalw

+ Công cụ dòng lệnh EMBOSS

– Một lớp chuẩn cho việc giải trình tự để xử lý các công việc liên quan đến giải trình tự, đánh id trên trình tự, và các đặc điểm của trình tự

– Các công cụ để thực hiện các thao tác trên trình tự như translation [dịch mã], trancription [phiên mã] và weight calculations [tính kích thước]

– Mã phân loại dữ liệu sử dụng K-Nearest Neighbors, Naives Bayes hay Support Vector Machines

– Mã để alignment [gióng hàng], gồm 1 cách chuẩn để tạo và xử lý các ma trận thay thế

– Mã để có thể dễ dàng chia các công việc có thể thực song song thành các luồng xử lý riêng biệt

– Chương trình có giao diện để làm các thao tác xử lý trình tự cơ bản, dịch mã, BLASTing, v. v

– Tài liệu mở rộng và hướng dẫn sử dụng các module, bao gồm tài liệu wiki trực tuyến, website và danh sách mail

One of the most important things in this module is the MultipleSeqAlignment class, used in the Bio. AlignIO module

class

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

2 [records , alphabet=None , annotations=None , column_annotations=None]¶

căn cứ.

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

Represents a classical multiple sequence alignment [MSA]

By this we mean a collection of sequences [usually shown as rows] which are all the same length [usually with gap characters for insertions or padding]. The data can then be regarded as a matrix of letters, with well defined columns

You would typically create an MSA by loading an alignment file with the AlignIO module

>>> from Bio import AlignIO
>>> align = AlignIO.read["Clustalw/opuntia.aln", "clustal"]
>>> print[align]
SingleLetterAlphabet[] alignment with 7 rows and 156 columns
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAG...AGA gi|6273291|gb|AF191665.1|AF191

In some respects you can treat these objects as lists of SeqRecord objects, each representing a row of the alignment. Iterating over an alignment gives the SeqRecord object for each row

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

You can also access individual rows as SeqRecord objects via their index

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

And extract columns as strings

>>> print[align[:, 1]]
AAAAAAA

Or, take just the first ten columns as a sub-alignment

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

Combining this alignment slicing with alignment addition allows you to remove a section of the alignment. For example, taking just the first and last ten columns

________số 8

Note - This object replaced the older Alignment object defined in module Bio. Căn chỉnh. Generic but is not fully backwards compatible with it

Note - This object does NOT attempt to model the kind of alignments used in next generation sequencing with multiple sequencing reads which are much shorter than the alignment, and where there is usually a consensus or reference sequence with special status

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

4 [self , records , alphabet=None , annotations=None , column_annotations=None]¶

Initialize a new MultipleSeqAlignment object

Tranh luận

records - A list [or iterator] of SeqRecord objects, whose
sequences are all the same length. This may be an be an empty list
alphabet - The alphabet for the whole alignment, typically a gapped
alphabet, which should be a super-set of the individual record alphabets. If omitted, a consensus alphabet is used
annotations - Information about the whole alignment [dictionary]
column_annotations - Per column annotation [restricted dictionary]
This holds Python sequences [lists, strings, tuples] whose length matches the number of columns. A typical use would be a secondary structure consensus string

You would normally load a MSA from a file using Bio. AlignIO, but you can do this from a list of SeqRecord objects too

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

0property

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

5¶

Dictionary of per-letter-annotation for the sequence

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

6 [self]¶

Return a multi-line string summary of the alignment

This output is intended to be readable, but large alignments are shown truncated. A maximum of 20 rows [sequences] and 50 columns are shown, with the record identifiers. This should fit nicely on a single screen. e. g

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

See also the alignment’s format method

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

7 [self]¶

Return a representation of the object for debugging

The representation cannot be used with eval[] to recreate the object, which is usually possible with simple python ojects. For example

The hex string is the memory address of the object, see help[id]. This provides a simple way to visually distinguish alignments of the same size

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

8 [self , format]¶

Return the alignment as a string in the specified file format

The format should be a lower case string supported as an output format by Bio. AlignIO [such as “fasta”, “clustal”, “phylip”, “stockholm”, etc], which is used to turn the alignment into a string

e. g

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

For Python 2. 6, 3. 0 or later see also the built in format[] function

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

9 [self , format_spec]¶

Return the alignment as a string in the specified file format

This method supports the python format[] function added in Python 2. 6/3. 0. The format_spec should be a lower case string supported by Bio. AlignIO as an output file format. See also the alignment’s format[] method

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

0 [self]¶

Iterate over alignment rows as SeqRecord objects

e. g

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

1 [self]¶

Return the number of sequences in the alignment

Use len[alignment] to get the number of sequences [i. e. the number of rows], and alignment. get_alignment_length[] to get the length of the longest sequence [i. e. the number of columns]

This is easy to remember if you think of the alignment as being like a list of SeqRecord objects

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

2 [self]¶

Return the maximum length of the alignment

All objects in the alignment should [hopefully] have the same length. This function will go through and find this length by finding the maximum length of sequences in the alignment

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

If you want to know the number of sequences in the alignment, use len[align] instead

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

3 [self , descriptor , sequence , start=None , end=None , weight=1. 0]¶

Add a sequence to the alignment

This doesn’t do any kind of alignment, it just adds in the sequence object, which is assumed to be prealigned with the existing sequences

Tranh luận

descriptor - The descriptive id of the sequence being added. This will be used as the resulting SeqRecord’s. id property [and, for historical compatibility, also the. description property]
sequence - A string with sequence info
start - You can explicitly set the start point of the sequence. This is useful [at least] for BLAST alignments, which can just be partial alignments of sequences
end - Specify the end of the sequence, which is important for the same reason as the start
weight - The weight to place on the sequence in the alignment. By default, all sequences have the same weight. [0. 0 => no weight, 1. 0 => highest weight]

In general providing a SeqRecord and calling. append is preferred

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

4 [self , records]¶

Add more SeqRecord objects to the alignment as rows

They must all have the same length as the original alignment, and have alphabets compatible with the alignment’s alphabet. For example,

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

First we create a small alignment [three rows]

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

Now we can extend this alignment with another two rows

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

Because the alignment object allows iteration over the rows as SeqRecords, you can use the extend method with a second alignment [provided its sequences have the same length as the original alignment]

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

5 [self , record]¶

Add one more SeqRecord object to the alignment as a new row

This must have the same length as the original alignment [unless this is the first record], and have an alphabet compatible with the alignment’s alphabet

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

We’ll now construct a dummy record to append as an example

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

Now append this to the alignment,

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

6 [self , other]¶

Combine two alignments with the same number of rows by adding them

If you have two multiple sequence alignments [MSAs], there are two ways to think about adding them - by row or by column. Using the extend method adds by row. Using the addition operator adds by column. For example,

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

Now, let’s look at these two alignments

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

And add them

>>> len[align]
7
>>> for record in align:
..     print["%s %i" % [record.id, len[record]]]
...
gi|6273285|gb|AF191659.1|AF191 156
gi|6273284|gb|AF191658.1|AF191 156
gi|6273287|gb|AF191661.1|AF191 156
gi|6273286|gb|AF191660.1|AF191 156
gi|6273290|gb|AF191664.1|AF191 156
gi|6273289|gb|AF191663.1|AF191 156
gi|6273291|gb|AF191665.1|AF191 156

For this to work, both alignments must have the same number of records [here they both have 3 rows]

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

The individual rows are SeqRecord objects, and these can be added together. Refer to the SeqRecord documentation for details of how the annotation is handled. This example is a special case in that both original alignments shared the same names, meaning when the rows are added they also get the same name

Any common annotations are preserved, but differing annotation is lost. This is the same behaviour used in the SeqRecord annotations and is designed to prevent accidental propagation of inappropriate values

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

Similarly any common per-column-annotations are combined

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

7 [self , index]¶

Access part of the alignment

Depending on the indices, you can get a SeqRecord object [representing a single row], a Seq object [for a single columns], a string [for a single characters] or another alignment [representing some part or all of the alignment]

align[r,c] gives a single character as a string align[r] gives a row as a SeqRecord align[r,. ] gives a row as a SeqRecord align[. ,c] gives a column as a Seq [using the alignment’s alphabet]

căn chỉnh [. ] and align[. ,. ] give a copy of the alignment

Anything else gives a sub alignment, e. g. căn chỉnh [0. 2] or align[0. 2,. ] uses only row 0 and 1 align[. ,1. 3] uses only columns 1 and 2 align[0. 2,1. 3] uses only rows 0 & 1 and only cols 1 & 2

We’ll use the following example alignment here for illustration

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

You can access a row of the alignment as a SeqRecord using an integer index [think of the alignment as a list of SeqRecord objects here]

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

You can also access use python’s slice notation to create a sub-alignment containing only some of the SeqRecord objects

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

This includes support for a step, i. e. align[start. chấm dứt. step], which can be used to select every second sequence

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

Or to get a copy of the alignment with the rows in reverse order

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

You can also use two indices to specify both rows and columns. Using simple integers gives you the entry as a single character string. e. g

This is equivalent to

hoặc

To get a single column [as a string] use this syntax

Or, to get part of a column,

However, in general you get a sub-alignment,

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

This should all seem familiar to anyone who has used the NumPy array or matrix objects

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

8 [self , key=None , reverse=False]¶

Sort the rows [SeqRecord objects] of the alignment in place

This sorts the rows alphabetically using the SeqRecord object id by default. The sorting can be controlled by supplying a key function which must map each SeqRecord to a sort value

This is useful if you want to add two alignments which use the same record identifiers, but in a different order. For example,

>>> print[align[0].id]
gi|6273285|gb|AF191659.1|AF191
>>> print[align[-1].id]
gi|6273291|gb|AF191665.1|AF191

If you simple try and add these without sorting, you get this

>>> print[align[:, 1]]
AAAAAAA

Consult the SeqRecord documentation which explains why you get a default value when annotation like the identifier doesn’t match up. However, if we sort the alignments first, then add them we get the desired result

>>> print[align[:, 1]]
AAAAAAA

As an example using a different sort order, you could sort on the GC content of each sequence

>>> print[align[:, 1]]
AAAAAAA

There is also a reverse argument, so if you wanted to sort by ID but backwards

>>> print[align[:, 1]]
AAAAAAA

3class

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

00 [target , query , path , score]¶

căn cứ.

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

Represents a pairwise sequence alignment

Internally, the pairwise alignment is stored as the path through the traceback matrix, i. e. a tuple of pairs of indices corresponding to the vertices of the path in the traceback matrix

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

4 [self , target , query , path , score]¶

Initialize a new PairwiseAlignment object

Tranh luận

target - The first sequence, as a plain string, without gaps
query - The second sequence, as a plain string, without gaps
path - The path through the traceback matrix, defining an
căn chỉnh
score - The alignment score

You would normally obtain a PairwiseAlignment object by iterating over a PairwiseAlignments object

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

03 [self , other] ¶

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

04 [self , other]¶

Return self==value

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

05 [self , other]¶

Return self. = giá trị

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

06 [self , other]¶

Return self>> print[align[:, :10]] SingleLetterAlphabet[] alignment with 7 rows and 10 columns TATACATTAA gi|6273285|gb|AF191659.1|AF191 TATACATTAA gi|6273284|gb|AF191658.1|AF191 TATACATTAA gi|6273287|gb|AF191661.1|AF191 TATACATAAA gi|6273286|gb|AF191660.1|AF191 TATACATTAA gi|6273290|gb|AF191664.1|AF191 TATACATTAA gi|6273289|gb|AF191663.1|AF191 TATACATTAA gi|6273291|gb|AF191665.1|AF191 07 [self , other]¶

Return self>value

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

09 [self , other]¶

Return self>=value

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

9 [self , format_spec]¶

Default object formatter

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

6 [self]¶

Return str[self]

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

8 [self]¶

Create a human-readable representation of the alignment

property

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

33¶

Return the indices of subsequences aligned to each other

This property returns the start and end indices of subsequences in the target and query sequence that were aligned to each other. If the alignment between target [t] and query [q] consists of N chunks, you get two tuples of length N

[[[t_start1, t_end1], [t_start2, t_end2], …, [t_startN, t_endN]],
[[q_start1, q_end1], [q_start2, q_end2], …, [q_startN, q_endN]]]

For example,

>>> print[align[:, 1]]
AAAAAAA

Note that different alignments may have the same subsequences aligned to each other. In particular, this may occur if alignments differ from each other in terms of their gap placement only

>>> print[align[:, 1]]
AAAAAAA

The property can be used to identify alignments that are identical to each other in terms of their aligned sequences

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

34 = None¶ class

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

36 [seqA , seqB , score , paths]¶

căn cứ.

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

Implements an iterator over pairwise alignments returned by the aligner

This class also supports indexing, which is fast for increasing indices, but may be slow for random access of a large number of alignments

Note that pairwise aligners can return an astronomical number of alignments, even for relatively short sequences, if they align poorly to each other. We therefore recommend to first check the number of alignments, accessible as len[alignments], which can be calculated quickly even if the number of alignments is very large

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

4 [self , seqA , seqB , score , paths]¶

Initialize a new PairwiseAlignments object

Tranh luận

seqA - The first sequence, as a plain string, without gaps
seqB - The second sequence, as a plain string, without gaps
score - The alignment score
paths - An iterator over the paths in the traceback matrix;
each path defines one alignment

You would normally obtain an PairwiseAlignments object by calling aligner. align[seqA, seqB], where aligner is a PairwiseAligner object

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

1 [self] ¶

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

7 [self , index] ¶

>>> print[align[:, :10] + align[:, -10:]]
SingleLetterAlphabet[] alignment with 7 rows and 20 columns
TATACATTAAGTGTACCAGA gi|6273285|gb|AF191659.1|AF191
TATACATTAAGTGTACCAGA gi|6273284|gb|AF191658.1|AF191
TATACATTAAGTGTACCAGA gi|6273287|gb|AF191661.1|AF191
TATACATAAAGTGTACCAGA gi|6273286|gb|AF191660.1|AF191
TATACATTAAGTGTACCAGA gi|6273290|gb|AF191664.1|AF191
TATACATTAAGTATACCAGA gi|6273289|gb|AF191663.1|AF191
TATACATTAAGTGTACCAGA gi|6273291|gb|AF191665.1|AF191

0 [self] ¶

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

62 [self]¶ class

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

64¶

căn cứ.

>>> print[align[:, :10]]
SingleLetterAlphabet[] alignment with 7 rows and 10 columns
TATACATTAA gi|6273285|gb|AF191659.1|AF191
TATACATTAA gi|6273284|gb|AF191658.1|AF191
TATACATTAA gi|6273287|gb|AF191661.1|AF191
TATACATAAA gi|6273286|gb|AF191660.1|AF191
TATACATTAA gi|6273290|gb|AF191664.1|AF191
TATACATTAA gi|6273289|gb|AF191663.1|AF191
TATACATTAA gi|6273291|gb|AF191665.1|AF191

Performs pairwise sequence alignment using dynamic programming

This provides functions to get global and local alignments between two sequences. A global alignment finds the best concordance between all characters in two sequences. A local alignment finds just the subsequences that align the best

To perform a pairwise sequence alignment, first create a PairwiseAligner object. This object stores the match and mismatch scores, as well as the gap scores. Typically, match scores are positive, while mismatch scores and gap scores are negative or zero. By default, the match score is 1, and the mismatch and gap scores are zero. Based on the values of the gap scores, a PairwiseAligner object automatically chooses the appropriate alignment algorithm [the Needleman-Wunsch, Smith-Waterman, Gotoh, or Waterman-Smith-Beyer global or local alignment algorithm]

Calling the “score” method on the aligner with two sequences as arguments will calculate the alignment score between the two sequences. Calling the “align” method on the aligner with two sequences as arguments will return a generator yielding the alignments between the two sequences

Some examples

>>> print[align[:, 1]]
AAAAAAA

Specify the aligner mode as local to generate local alignments

>>> print[align[:, 1]]
AAAAAAA

Do a global alignment. Identical characters are given 2 points, 1 point is deducted for each non-identical character

>>> print[align[:, 1]]
AAAAAAA

Same as above, except now 0. 5 points are deducted when opening a gap, and 0. 1 points are deducted when extending it

Biopython nghe lén

Bài Viết Liên Quan

Dụng javascript lấy dữ liệu từ form

3 tỷ bằng bao nhiêu đô la

Tự động làm mới phần tử html

Khởi động php: không thể tải thư viện động mysqli đã thử usr lib64 php/mô-đun mysqli

Does the 2023 Kia Sportage have blind

Thuộc tính dữ liệu trong python là gì?

Làm cách nào để kiểm tra xem địa chỉ ip có trong mạng trong python không?

Có thể tạo một trang web không có html không?

Nguồn dữ liệu odbc mysql

Bảng lịch thi đấu MLB 2023

Báo cáo trăn pdf

Làm thế nào để bạn tạo hello world trong html?

Cạo zillow dữ liệu python

Chuyển đổi int thành python nhị phân 8 bit

Cách đếm tháng trong Google Sheets

Tìm vị trí của một từ trong chuỗi python

Cách xóa thẻ html trong jquery?

Lặp qua python

Php_xmlrpc dll php 8

Events in Europe 2023

Toplist mới

Top 7 sự tích hồ gươm - ngữ văn lớp 6 2023

Top 7 gdcd 6 bài 1 kết nối tri thức 2023

Top 7 ý nghĩa của xây dựng gia đình văn hóa 2023

Top 6 mẫu hợp đồng mượn đất làm nhà xưởng 2023

Top 3 tổng tài biến thái tôi yêu anh tập 27 2023

Top 6 kết thực phim mỹ nhân vô lệ 2023

Top 9 trong những câu thơ sau câu nào sử dụng thành ngữ 2023

Top 8 đề tài và chủ de của tác phẩm tắt đèn 2023

Top 5 tiểu sử của thầy thích pháp hòa 2023

Bài mới nhất

Ăn táo đỏ lúc nào là tốt nhất năm 2024

Hướng dẫn tính trung bình cộng trong excel năm 2024

Cách conditonal fortmatting cho ô chứa lỗi thành màu trằng năm 2024

Khi chạy chương trình báo lỗi invalid missing system.setup năm 2024

Bài giảng sự lai hóa các obitan phân tử năm 2024

Chủ Đề