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Biopython Tutorial and Cookbook和訳(4.1)


  • 生物の学習
  • Biopythonの勉強
  • 英語の復習
  • 少しでもこの分野に貢献したい


 Chapter 4 Sequence annotation objects

Chapter 3 introduced the sequence classes.

Immediately “above” the Seq class is the Sequence Record or SeqRecord class, defined in the Bio.SeqRecord module.
Seq classの真上(継承の意味?)はSequence Record、あるいはSeqRecordクラス、Bio.SeqRecordモジュール内に定義されています。

This class allows higher level features such as identifiers and features (as SeqFeature objects) to be associated with the sequence, and is used throughout the sequence input/output interface Bio.SeqIO described fully in Chapter 5.
このクラスはidentifiersやfeature(SeqFeatureオブジェクト)のようなハイレベルの特徴をシーケンスと結びつける、そしてchap5に紹介するシーケンスのinput/outputインタフェース - Bio.SeqIOに広く使われています。

If you are only going to be working with simple data like FASTA files, you can probably(おそらく) skip this chapter for now.

While this chapter should cover most things to do with the SeqRecord and SeqFeature objects in this chapter,
you may also want to read the SeqRecord wiki page (http://biopython.org/wiki/SeqRecord), and the built in documentation (also online – SeqRecord and SeqFeature):
この章ではSeqRecord や SeqFeature objectsを使って多くのことをこなす必要があり、
SeqRecord wiki pageや関数のドキュメンテーションも参照したほうがいいかもしれないです。

>>> from Bio.SeqRecord import SeqRecord
>>> help(SeqRecord)

 4.1 The SeqRecord object

The SeqRecord (Sequence Record) class is defined in the Bio.SeqRecord module.
SeqRecord (Sequence Record)クラスはBio.SeqRecordモジュール内に定義されています。

This class allows higher level features such as identifiers and features to be associated with a sequence (see Chapter 3),
and is the basic data type for the Bio.SeqIO sequence input/output interface (see Chapter 5).

The SeqRecord class itself is quite simple, and offers the following information as attributes:

– The sequence itself, typically a Seq object.
– The primary ID used to identify the sequence – a string. In most cases this is something like an accession number.
– A “common” name/id for the sequence – a string. In some cases this will be the same as the accession number, but it could also be a clone name. I think of this as being analogous to the LOCUS id in a GenBank record.
– A human readable description or expressive name for the sequence – a string.
– Holds per-letter-annotations using a (restricted) dictionary of additional information about the letters in the sequence. The keys are the name of the information, and the information is contained in the value as a Python sequence (i.e. a list, tuple or string) with the same length as the sequence itself. This is often used for quality scores (e.g. Section 20.1.6) or secondary structure information (e.g. from Stockholm/PFAM alignment files).
– A dictionary of additional information about the sequence. The keys are the name of the information, and the information is contained in the value. This allows the addition of more “unstructured” information to the sequence.
– A list of SeqFeature objects with more structured information about the features on a sequence (e.g. position of genes on a genome, or domains on a protein sequence). The structure of sequence features is described below in Section 4.3.
- A list of database cross-references as strings.

– シーケンス自分自身, 一般的にSeqオブジェクト.
– シーケンスを識別するためのID – 文字列. 多くの場合はアクセッション番号.
– シーケンスの通称 – 文字列. たまにはアクセッション番号かクローンネームとなります('Clone name'が'IR'で始まるクローンが完全長クローンです). GenBank recordの遺伝子座IDに似ています.
– 人間が可読な情報 あるいはシーケンスの意味を表す名前 – 文字列.
– (制限された)シーケンスの文字に関する付加情報(辞書型)を利用することで文字ごとのアノテーションを保持します. キーは情報の名前で, 情報は値に含まれます (i.e. リスト、タプルあるいは文字列) シーケンスと同じ長さになります. 品質スコア (e.g. Section 20.1.6) あるいは二次構造情報によく使われます (e.g. from Stockholm/PFAM alignment files).
– シーケンス付加情報(辞書型). キーは情報の名前, 値は情報. シーケンスにより多くの付加情報を追加することができます.
– SeqFeature objectsのリスト型でより多くの構造化情報が含まれるシーケンスの特徴データ (e.g. ゲノム上の遺伝子位置情報, あるいはたんぱく質シーケンスのドメイン). Section 4.3では構造化したシーケンスの特徴を言及します.
– データベースの相互参照リスト(文字列).


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