LargeScaleSequencing를 위한 FragmentAssembly프로그램. 최근에는 [Phrap]을 능가하는 오일러 라는 프로그램도 소개된바 있다. PhilGreen박사 작성

http://www.phrap.org/

보통 다음의 파이프라인을 구성한다. {{| [Phred] - CrossMatch - RepeatMasker - [Phrap] - [Consed] |}}

특별한 상황을 위한 추가프로그램들이 있다.

  • phrap.manyreads : reads갯수가 64,000개를 넘을때
  • phrap.longreads : 특정 reads의 길이가 64,000bp를 넘을때

참고정보


[Phrap]이 만든 ACE파일을 BioPython을 이용해서 [Parsing]하던중 에러발생. 보니깐 BioPython 소스의 문제다. 파서가 'CT'레코드 와 FastaFormatNucleicAcid서열 '^CT'를 구분하지 못하므로 생기는 문제. 곧바로 BioPython의 메일링리스트에 날렸다. :) 여기 메일링리스트에 메일쓰기는 처음. 이렇게 써버릇하면서 EnglishStudy도 하는거야 하면서 혼자 마냥 흐뭇한중 --[yong27/2004-04]

http://www.biopython.org/pipermail/biopython/2004-April/001998.html

{{| > I used v1.3(in CVS) and the newest is v1.5. > I could see their diffs in > http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Sequencing/Ace.py.diff?r1=1.3&r2=1.5&cvsroot=biopython >

Oh, there's also a typo in line 576, where it should read 'Missing header line in WA tag' instead of '... CT tag' :-(

> But, I also modified ace.py because Iterator class does not support iter. > I want to know why iter is depreciated although it is very convenient. >

Good question. I can't remember having removed iter by myself on purpose? Maybe I deleted it accidentially? Brad, do you know why iter is out of the Iterator class? However it is still possible to get throught the ace file contig by contig. But as explained in the header of Ace.py, as data related to a specific contig might be at the very end of the file, it is usually a better idea to use the ACEParser() and read the file at once, and then go through the contigs. This makes sure that all available data is included in the appropriate contig record.

Frank |}}


SeeAlso [CAP3]


CategoryProgramBio

Phrap (last edited 2011-08-03 11:00:35 by localhost)

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