perl_Blast策略.doc

/?_c11_BlogPart_pagedir=Next&_c11_BlogPart_handle=cns!E5D4E2743495BC95!617&_c11_BlogPart_BlogPart=blogview&_c=BlogPart1月26日Other profile HMM implementationsSource: /userguides/seq/hmmer/docs/node15.html Several implementations of profile HMM methods and related PSSM methods are available. Some are listed in the table below. Software URL HMMER / SAM /research/compbio/sam.html PFTOOLS http:/ulrec3.unil.ch:80/profile/ HMMpro /html/hmmpro.html GENEWISE http:/www.sanger.ac.uk/Software/Wise2/ PROBE /pub/neuwald/probe1.0/ META-MEME /users/bgrundy/metameme.1.0.html BLOCKS / PSI-BLAST /BLAST/newblast.htmlHMMER, SAM, PFTOOLS, and HMMpro are the most closely related to the profile HMM methods introduced by Krogh et al. HMMpro is commercial, not free software. 2:28| 添加评论| 固定链接| 写入日志HMM related softwareHMMER / SAM(Sequence Alignment and Modeling System) / HMMpro A windows version for HMM The Division of Biomedical Informatics at Cincinnati Childrens Hospital Medical Center metaMEME: A motif based Hidden Markov Model2:19| 添加评论| 固定链接| 写入日志An example for Bio:DB:Fastatags: fastacmd fasta seq fetch perl bioperl script#!/usr/bin/perluse strict;use Bio:DB:Fasta;use Bio:SeqIO;my $db = Bio:DB:Fasta-new(./dat/all.pep);#my ids = $db-ids;#print join(n,ids);my $f_seqout=./dat/wxs.fasta;my $oseqout=Bio:SeqIO-new(-file=$f_seqout,-format=fasta);open IN, ./dat/id.list;my $cnt=0;while () chomp;$_=s/st/gi;my $qid=$_;my $obj =undef;$obj=$db-get_Seq_by_id($qid);if (defined($obj) $oseqout-write_seq($obj);$cnt+=1;close IN;print $cnt;$oseqout-close;0:04| 添加评论| 固定链接| 写入日志1月23日危积于忽,功成乎细危险,都是在长期的日常的疏忽中积累的.圣人曰:人生最危险的事情,其实是在枕席餐桌之间.成功,都是在长期细节上的努力中累积的.本起于末,是事物发展的某种规律.12:50| 添加评论| 固定链接| 写入日志1月22日人和时代的三种关系顺潮流而动,最高境界是引导潮流.逆潮流而动,最高境界是冒天下之大不韪.自己创造潮流,最高境界是独树一帜,一呼百应.至于无所谓顺,逆,或者去创造,那就好像悠游在大海之上,.18:48| 添加评论| 固定链接| 写入日志perl script: web blast clientsource: /blast/documents/web_blast.pltags: remote web blast client ncbi #!/usr/bin/perl# $Id: web_blast.pl,v 1.3 2004/12/10 18:05:08 coulouri Exp $# =# PUBLIC DOMAIN NOTICE# National Center for Biotechnology Information# This software/database is a United States Government Work under the# terms of the United States Copyright Act. It was written as part of# the authors offical duties as a United States Government employee and# thus cannot be copyrighted. This software/database is freely available# to the public for use. The National Library of Medicine and the U.S.# Government have not placed any restriction on its use or reproduction.# Although all reasonable efforts have been taken to ensure the accuracy# and reliability of the software and data, the NLM and the U.S.# Government do not and cannot warrant the performance or results that# may be obtained by using this software or data. The NLM and the U.S.# Government disclaim all warranties, express or implied, including# warranties of performance, merchantability or fitness for any particular# purpose.# Please cite the author in any work or product based on this material.# =# This code is for example purposes only.# Please refer to /blast/Doc/urlapi.html# for a complete list of allowed parameters.# Please do not submit or retrieve more than one request every two seconds.# Results will be kept at NCBI for 24 hours. For best batch performance,# we recommend that you submit requests after 2000 EST (0100 GMT) and# retrieve results before 0500 EST (1000 GMT).# =# return codes:# 0 - success# 1 - invalid arguments# 2 - no hits found# 3 - rid expired# 4 - search failed# 5 - unknown error# =use URI:Escape;use LWP:UserAgent;use HTTP:Request:Common qw(POST);$ua = LWP:UserAgent-new;$ENVHTTP_PROXY=http:/xxxxxxxx:8080;$ua-timeout(800);$ua-env_proxy;$argc = $#ARGV + 1;if ($argc 3) ) print $program does not yet support multiple queries.n; exit 1; if ($program eq megablast) $program = blastn&MEGABLAST=on; if ($program eq rpsblast) $program = blastp&SERVICE=rpsblast; # read and encode the queriesforeach $query (ARGV) open(QUERY,$query); while() $encoded_query = $encoded_query . uri_escape($_); # build the request$args = CMD=Put&PROGRAM=$program&DATABASE=$database&QUERY= . $encoded_query;$req = new HTTP:Request POST = /blast/Blast.cgi;$req-content_type(application/x-www-form-urlencoded);$req-content($args);# get the response$response = $ua-request($req);# parse out the request id$response-content = / RID = (.*$)/m;$rid=$1;# parse out the estimated time to completion$response-content = / RTOE = (.*$)/m;$rtoe=$1;# wait for search to completesleep $rtoe;# poll for resultswhile (true) sleep 5; $req = new HTTP:Request GET = /blast/Blast.cgi?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=$rid; $response = $ua-request($req); if ($response-content = /tStatus=WAITING/m) # print STDERR Searching.n; next; if ($response-content = /tStatus=FAILED/m) print STDERR Search $rid failed; please report to .n; exit 4; if ($response-content = /tStatus=UNKNOWN/m) print STDERR Search $rid expired.n; exit 3; if ($response-content = /tStatus=READY/m) if ($response-content = /tThereAreHits=yes/m) # print STDERR Search complete, retrieving results.n; last; else print STDERR No hits found.n; exit 2; # if we get here, something unexpected happened. exit 5; # end poll loop# retrieve and display results$req = new HTTP:Request GET = /blast/Blast.cgi?CMD=Get&FORMAT_TYPE=Text&RID=$rid;$response = $ua-request($req);print $response-content;exit 0;#!/usr/bin/perl# $Id: web_blast.pl,v 1.3 2004/12/10 18:05:08 coulouri Exp $# =# PUBLIC DOMAIN NOTICE# National Center for Biotechnology Information# This software/database is a United States Government Work under the# terms of the United States Copyright Act. It was written as part of# the authors offical duties as a United States Government employee and# thus cannot be copyrighted. This software/database is freely available# to the public for use. The National Library of Medicine and the U.S.# Government have not placed any restriction on its use or reproduction.# Although all reasonable efforts have been taken to ensure the accuracy# and reliability of the software and data, the NLM and the U.S.# Government do not and cannot warrant the performance or results that# may be obtained by using this software or data. The NLM and the U.S.# Government disclaim all warranties, express or implied, including# warranties of performance, merchantability or fitness for any particular# purpose.# Please cite the author in any work or product based on this material.# =# This code is for example purposes only.# Please refer to /blast/Doc/urlapi.html# for a complete list of allowed parameters.# Please do not submit or retrieve more than one request every two seconds.# Results will be kept at NCBI for 24 hours. For best batch performance,# we recommend that you submit requests after 2000 EST (0100 GMT) and# retrieve results before 0500 EST (1000 GMT).# =# return codes:# 0 - success# 1 - invalid arguments# 2 - no hits found# 3 - rid expired# 4 - search failed# 5 - unknown error# =use URI:Escape;use LWP:UserAgent;use HTTP:Request:Common qw(POST);$ua = LWP:UserAgent-new;$ENVHTTP_PROXY=http:/xxxxxxxx:8080;$ua-timeout(800);$ua-env_proxy;$argc = $#ARGV + 1;if ($argc 3) ) print $program does not yet support multiple queries.n; exit 1; if ($program eq megablast) $program = blastn&MEGABLAST=on; if ($program eq rpsblast) $program = blastp&SERVICE=rpsblast; # read and encode the queriesforeach $query (ARGV) open(QUERY,$query); while() $encoded_query = $encoded_query . uri_escape($_); # build the request$args = CMD=Put&PROGRAM=$program&DATABASE=$database&QUERY= . $encoded_query;$req = new HTTP:Request POST = /blast/Blast.cgi;$req-content_type(application/x-www-form-urlencoded);$req-content($args);# get the response$response = $ua-request($req);# parse out the request id$response-content = / RID = (.*$)/m;$rid=$1;# parse out the estimated time to completion$response-content = / RTOE = (.*$)/m;$rtoe=$1;# wait for search to completesleep $rtoe;# poll for resultswhile (true) sleep 5; $req = new HTTP:Request GET = /blast/Blast.cgi?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=$rid; $response = $ua-request($req); if ($response-content = /tStatus=WAITING/m) # print STDERR Searching.n; next; if ($response-content = /tStatus=FAILED/m) print STDERR Search $rid failed; please report to .n; exit 4; if ($response-content = /tStatus=UNKNOWN/m) print STDERR Search $rid expired.n; exit 3; if ($response-content = /tStatus=READY/m) if ($response-content = /tThereAreHits=yes/m) # print STDERR Search complete, retrieving results.n; last; else print STDERR No hits found.n; exit 2; # if we get here, something unexpected happened. exit 5; # end poll loop# retrieve and display results$req = new HTTP:Request GET = /blast/Blast.cgi?CMD=Get&FORMAT_TYPE=Text&RID=$rid;$response = $ua-request($req);print $response-content;exit 0;12:08| 添加评论| 固定链接| 写入日志1月20日苦乐同质和悲剧美我只是自然的影子，道法自然。苦乐其实同质，在悲剧美中，怀报悲切之痛而心安。23:30| 添加评论| 固定链接| 写入日志1月19日解放思想,实事求是:解释(相对),策略(实用)和存在(实践)主义世界就是意志的角逐场.必须把人当物品看,物有物性,人有人性,不能有任何幻想.因为人都是有限的,有他的价值观,知识,经验,能力,思维和习惯上的局限性,并且受到其所在的社会环境,其所扮演的角色的制约.解放思想,实事求是,禀行解释(相对),策略(实用)和存在(实践)主义. 一切都是相对的,好和坏,对和错,往往都是相对特定主体而言.必须实行实用主义,即根据效果来决定心理和行为取向,作为一种存在物,而非超存在物,这是必须的.存在主义的核心在于,我们不是根据过去来决定行为和心理取向,而是根据未来,我们可以用行动来造就新的心理现实(状态,系统)和物质世界.18:11| 添加评论| 固定链接| 写入日志CFP, SDM07 Biomedical Informatics, Apr 2007: Announcement and call for papersCFP, SDM07 Biomedical Informatics, Apr 2007: Announcement and call for papersAnnouncement and call for papers:Data Mining for Biomedical Informatics, a full-day workshop, to be held inconjunction with the 7th SIAM International Conference on Data Mining (SDM2007) in Minneapolis, MN on April 28, 2007. For detailed information aboutthe workshop see /DMBIO/.Biology is rich in data, and is getting richer all the time. Deriving bigpictures from this sea of biomedical data is a major scientific challengethat will require the close collaboration of computer scientists,biologist