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云之南

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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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生物信息学应用工具汇总  

2009-12-08 13:58:38|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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人类基因信息数据库 - http://www.medicalcomputing.net/cgi-bin/query_human_gene_info, 医学计算,网络
基因组学在线数据库 - http://wit.integratedgenomics.com/GOLD
基因研究最新进展
联合基因组学会
基因组研究中心(TIGR) - http://www.tigr.org
桑格中心 - http://www.sanger.ac.uk
美国国家生物技术信息中心(NCBI) - http://www.ncbi.nlm.nih.gov


motivation:针对不同的生物信息学和生物学研究需要提供相应的web工具和
软件工具

notes:学习类资源(如教程、论坛、ftp等等)请到 5 网络资源 中寻找
学会使用google搜索自己需要的资源(参见精华区9-4-9)
web表示在线工具,local表示需下载后使用的软件工具
提供的某些软件为商业软件,请注意

目录如下:

>综合

>Alignment

>Pairwise alignment

>Sequence Viewers and editor

>Sequence format conversion tools

>Translation tool

>Sequence search

>Sequence search by Genome

>UTR analysis

>Signal Scan

>Promoter Scan

>Protein Motif&Domain analysis

>Transmembrane Domains

>Post-translational modifications

>Structural Analysis

>Structure prediction

>Contig assembly

>Primer design

>Restriction Analysis

>Molecular Evolution

>Phylogeny

>Molecular modelling and graphics

>Sequence data submissions

>Miscellaneous Tools

>综合
NCBI
web
www.ncbi.nlm.nih.gov
EBI
web
www.ebi.ac.uk
CBI
web
www.cbi.pku.edu.cn
ExPASy Proteomics tools
web
http://ca.expasy.org/tools/
EMBOSS
web
http://www.ebi.ac.uk/emboss/
http://211.161.196.209/w2h/
local
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/
http://www.emboss.org/
Web-based Sequence Analysis
web
http://analysis.molbiol.ox.ac.uk/pise_html/index.html
BCM Search Launcher
web
http://searchlauncher.bcm.tmc.edu/
local
ftp://ftp.hgsc.bcm.tmc.edu/sl/software/search-launcher/
Pasteur Institute
web
http://bioweb.pasteur.fr/intro-uk.html
SeWeR
web
http://iubio.bio.indiana.edu/webapps/SeWeR/
The Sequence Manipulation Suite
web
http://www.ualberta.ca/~stothard/javascript/index.html
CBS Prediction Servers
web
http://www.cbs.dtu.dk/services/
CMS Molecular Biology Resource
web
http://restools.sdsc.edu/
>Alignment
ClustalW
web
http://www.ebi.ac.uk/cgi-bin/newclustalw.pl
DCA
web
http://bibiserv.techfak.uni-bielefeld.de/dca/
SIM4
web
http://biom3.univ-lyon1.fr/sim4.html
SIM
web
http://ca.expasy.org/tools/sim-prot.html
DIALIGN
web
http://bibiserv.techfak.uni-bielefeld.de/cgi-bin/dialign_submit

>Pairwise alignment
bl2seq
web
http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html
align
web
http://www.ebi.ac.uk/emboss/align/

>Sequence Viewers and editor
GeneDoc
local
http://www.psc.edu/biomed/genedoc/
CHROMA
local
http://www.lg.ndirect.co.uk/chroma/
BioEdit
local
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
>Sequence format conversion tools
READSEQ
web
http://bimas.dcrt.nih.gov/molbio/readseq/
Reverse Complement
web
http://www.bioinformatics.vg/bio ... s/reversecomplement
.htm
Reverse Complement
web
http://www.ualberta.ca/~stothard/javascript/rev_comp.html
RevComp
local
http://www.cmrsinc.com/sequence/RevComp.exe
>Translation tool
Transeq
web
http://www.ebi.ac.uk/emboss/transeq/index.html
Translate
web
http://us.expasy.org/tools/dna.html
Translation Machine
web
http://www2.ebi.ac.uk/translate/
DNA Sequence Translator
web
http://biocommons.bcc.washington ... oftware/dnatranslat
or/index.html
>Sequence search
BLAST
web
http://www.ncbi.nlm.nih.gov/BLAST/
local
NCBI-Blast ftp://ftp.ncbi.nlm.nih.gov/blast/
WU-Blast http://blast.wustl.edu/
Fasta
web
http://www.ebi.ac.uk/fasta33/index.html
MPsrch
web
http://www.ebi.ac.uk/MPsrch/index.html
Smith-Waterman Reverse-Frame Search
web
http://www.dna.affrc.go.jp/htbin/tswn.pl
ESTblast
web
http://www.hgmp.mrc.ac.uk/ESTBlast/
>Sequence search by Genome
NCBI:Genomic BLAST pages
web
http://www.ncbi.nlm.nih.gov/BLAST/
GOLD
web
http://wit.integratedgenomics.com/GOLD/

>UTR analysis
UTRhome
http://bighost.area.ba.cnr.it/BIG/UTRHome/
>Signal Scan
SignalP
web
http://www.cbs.dtu.dk/services/SignalP-2.0/
http://bimas.dcrt.nih.gov/molbio/signal/
http://www.dna.affrc.go.jp/htdocs/sigscan/signal.html
local
Send inquiries by e-mail to software@cbs.dtu.dk .
TargetP
web
http://www.cbs.dtu.dk/services/TargetP/
SIGSCAN
web
http://bimas.dcrt.nih.gov/molbio/signal/
ChloroP
web
http://www.cbs.dtu.dk/services/ChloroP/
NetPhos
web
http://www.cbs.dtu.dk/services/NetPhos/
>Promoter Scan
PROSCAN
web
http://bimas.dcrt.nih.gov/molbio/proscan/
TRANSFAC
web
http://transfac.gbf.de/TRANSFAC/
COMPEL
web
http://compel.bionet.nsc.ru/compel/compel.html
local
http://compel.bionet.nsc.ru/cgi-bin/download/download.pl
Promoter 2.0
web
http://www.cbs.dtu.dk/services/Promoter/
PROMOTER SCAN II
web
http://www.molbiol.ox.ac.uk/promoterscan.htm
Promoter Prodiction
web
http://www.fruitfly.org/seq_tools/promoter.html
>Protein Motif&Domain analysis
InterProScan
web
http://www.ebi.ac.uk/interpro/scan.html
local
ftp://ftp.ebi.ac.uk/pub/databases/interpro/
SMART
web
http://smart.embl-heidelberg.de/
PROSITE
web
http://us.expasy.org/prosite/
local
http://us.expasy.org/ftp/databases/prosite/
Pfam
web
http://pfam.wustl.edu/
local
ftp://ftp.genetics.wustl.edu/pub/Pfam/
CDD
web
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
PRINTS
web
http://bioinf.man.ac.uk/dbbrowser/PRINTS/
ProDom
web
http://prodes.toulouse.inra.fr/prodom/2002.1/html/home.php
ELM
web
http://elm.eu.org/
TIGRFAMs
web
http://www.tigr.org/TIGRFAMs/
local
ftp://ftp.tigr.org/pub/data/TIGRFAMs
>Transmembrane Domains
TMHMM
web
http://www.cbs.dtu.dk/services/TMHMM-2.0/
PRED-TMR
web
http://o2.db.uoa.gr/PRED-TMR/
DAS
web
http://www.sbc.su.se/~miklos/DAS/
TopPred
web
http://www.sbc.su.se/~erikw/toppred2/
TMpred
web
http://www.ch.embnet.org/software/TMPRED_form.html
>Post-translational modifications
YinOYang
web
http://www.cbs.dtu.dk/services/YinOYang/
GlycoMod
web
http://ca.expasy.org/tools/glycomod/
FindMod
web
http://ca.expasy.org/tools/findmod/
PhosphoBase
web
http://www.cbs.dtu.dk/databases/PhosphoBase/
O-GlycBase
web
http://www.cbs.dtu.dk/databases/OGLYCBASE/
NetOGlyc
web
http://www.cbs.dtu.dk/services/NetOGlyc/
NetPhos
web
http://www.cbs.dtu.dk/services/NetPhos/

>Structural Analysis
RasMol
local
http://openrasmol.org/
MolScript
local
http://www.avatar.se/molscript/
Cn3D
local
http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
36m Raster3D
local
http://www.bmsc.washington.edu/raster3d/raster3d.html
Swiss-PdbViewer
local
http://us.expasy.org/spdbv/
>Structure prediction
SWISS-MODEL
web
http://www.expasy.org/swissmod/
HMMSTR/I-sites/Rosetta Prediction Server
web
http://www.bioinfo.rpi.edu/~bystrc/hmmstr/server.php
UCLA/DOE Fold Server
web
http://fold.doe-mbi.ucla.edu/
>Contig assembly
CAP3
web
http://pbil.univ-lyon1.fr/cap3.html
>Primer design
primer3
web
http://biocore.unl.edu/cgi-bin/primer3/primer3_www.cgi
Oligo
local
http://www.oligo.net/
Primer Premier
local
http://www.PremierBiosoft.com/
Oligo Analyzer3.0
web
http://207.32.43.70/biotools/oligocalc/oligocalc.asp
Fast PCR
local
http://www.biocenter.helsinki.fi/bi/bare-1_html/oligos.htm
>Restriction Analysis
REBASE
web
http://rebase.neb.com/rebase/rebase.html
Rsites
web
http://biotools.umassmed.edu/bioapps/rsites.html
Webcutter
web
http://www.ccsi.com/firstmarket/cutter/cut2.html
NEBcutter
web
http://tools.neb.com/NEBcutter/index.php3
RestrictionMapper
web
http://www.restrictionmapper.org/
SILENT
web
http://bioweb.pasteur.fr/seqanal/interfaces/silent.html
pDRAW32
local
http://www.acaclone.com/
DNAsis
local
http://www.oligo.net/dnasis.htm
>Phylogeny
Phylip
web
http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html
local
http://evolution.genetics.washington.edu/phylip.html
TreeView
local
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
fastDNAml
web
http://bioweb.pasteur.fr/seqanal/interfaces/fastdnaml.html
TreeTop
web
http://www.genebee.msu.su/services/phtree_reduced.html
Phylodendron
web
http://iubio.bio.indiana.edu/treeapp/treeprint-form.html
local
http://iubio.bio.indiana.edu/treeapp/
>codon usage
Countcodon
web
http://www.kazusa.or.jp/codon/countcodon.html
codonw
web
http://bioweb.pasteur.fr/seqanal/interfaces/codonw.html
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