Related Databases/Websites

Sequence

Bioinformatics Tools for Multiple Sequence Alignment EBI
Bioinformatics Tools for Pairwise Sequence Alignment EBI
BLAST
ClustalW and ClustalX Multiple Sequence Alignment
ClustalW2 EBI
EBI Global or local alignment
ExPASy – Translate tool
FASTA Tools for Sequence Similarity Searching Protein or Nucleotide
Databases EBI
http–sonnhammer.sbc.su.se-Dotter.html
http–www.bii.a-star.edu.sg-achievements-applications-clustalw-index.php
IBIVU Server – PRALINE Multiple Sequence Alignment
LALIGN Server
MAFFT Fast Multiple Alignment Tools for Large Batches of Sequences EBI
Mobyle portal – combat
mpiBLAST About – Overview
MUSCLE Multiple Accurate and Fast Sequence Comparison by Log-Expectation Tool EBI
Nucleotide BLAST Align two or more sequences using BLAST
Repbase – GIRI
SeaView
Sequence Massager
SIM4 – align cDNA and genomic DNA
SSEARCH Tool for Similarity & Homology Searching EBI
Tcoffee MSA
Tcoffee

 BLAST 本地化

Windows平台下新版blast(2.2.24+)本地化

Linux系统中NCBI BLAST+本地化教程

Algorithm

APPLICATIONS OF MULTIPLE ALIGNMENT

http–www.genome.jp-aaindex-AAindex-list_of_matrices

The R Project for Statistical Computing

Viterbi Algorithm

DNA

COGs – Clusters of Orthologous Groups

DNA Kit DNA Testing Kit DNA Kits – Send back with payment

ExPASy – PROSITEGenetic Testing for Health, Disease & Ancestry;

DNA Test – 23andMeIntegrated DNA Technologies

KEGG GENES Database

National Center for Biotechnology InformationNCBI HomePage

p-pod Princeton Protein Orthology Database

PACdb PolyA Cleavage Site & 3′ UTR Database

Sequence MassagerTreeFam

Gene

Digital Differential Display

DRAGON Database

Gene Expression Omnibus (GEO) Main page

Gene Home

Gene Ontology

GeneCards V3 – Human Genes Gene Database Gene Search

geneid WEB serverHGNC Home Page

kegg Kyoto Encyclopedia of Genes and Genomes

National Center for Biotechnology Information

UniGene Home

Codon Usage/ Codon Bias

Codon Usage Database

Codon Usage Analyzer

Genome

dogma Annotation of Chloroplast and Animal Mitochondrial Genomes

ENCODE Project at UCSC

Ensembl Genome

BrowserEntrez Genome view

kegg Kyoto Encyclopedia of Genes and Genomes

UCSC Genome Browser Home

Vega Genome Browser

VISTA tools

Genome Assembler

Velvet: http://www.ebi.ac.uk/~zerbino/velvet/

ABYSS: http://www.bcgsc.ca/platform/bioinfo/software/abyss

SOAPdenovo(华大基因): http://soap.genomics.org.cn/soapdenovo.html

ALLPATHS: http://tinyurl.com/3htptdz

CLC NGS Cell,商业软件: http://www.clcbio.com/index.php?id=1331

Curtaina,基于Velvet的Pipeline: http://code.google.com/p/curtain/

Edena: http://www.genomic.ch/edena.php

Euler-SR: http://euler-assembler.ucsd.edu/portal/

FuzzyPathftp://ftp.sanger.ac.uk/pub/zn1/fuzzypath/

Oasesb: http://www.ebi.ac.uk/~zerbino/oases/

QSRA: http://qsra.cgrb.oregonstate.edu/

SeqCons: http://www.seqan.de/projects/seqcons.html

SHARCGS: http://sharcgs.molgen.mpg.de/

SHORTY: http://www.cs.sunysb.edu/~skiena/shorty/

SOPRA: http://www.physics.rutgers.edu/~anirvans/SOPRA/

SSAKE: http://www.bcgsc.ca/platform/bioinfo/software/ssake

Taipan: http://taipan.sourceforge.net/

VCAKE: http://sourceforge.net/projects/vcake/

Comparative genomics

VISTA http://genome.lbl.gov/vista/index.shtml

ACT http://www.webact.org/WebACT/home

MUMMER http://mummer.sourceforge.net/

MAUVE http://darlinglab.org/mauve/mauve.html

Twin-SCAN/N-SCAN http://mblab.wustl.edu/software.html

 Microbiology

HIV Databases
PARTIC :Pathosystem Resource integration Center

RNA Folding

The DINAMelt Web Serverhttp://unafold.rna.albany.edu/?q=DINAMelt

The mfold Web Server http://unafold.rna.albany.edu/?q=mfold

miRNA

DIANA LAB – DNA Intelligent Analysis

Main Page – miRDB

Microcosm Targets

miRBase

miRecords

Segal Lab microRNA 2007 – Download Predictions

TargetScanHuman 5.1

Perl

Getting BioPerl – BioPerl
PerlChina.org – wiki – BioPerl安装
The Perl Programming Language – www.perl.org

Phylogeny

MEGA Molecular Evolutionary Genetics Analysis
phyloXML XML for evolutionary biology and comparative genomics

Protein&Protomics

A primer on UniProtKB–Swiss-Prot annotation
ExPASy – PROSITE
ExPASy – ProtScale
ExPASy – SWISS-2DPAGE top page
ExPASy – Tools
ExPASy Proteomics Server
HAMAP
iHOP – Information Hyperlinked over Proteins [ ELP2P ]
Interpro Protein sequence analysis & classification
IPI International Protein Index EBI
NCBI VAST Home Page
Pfam Home page
PredictProtein – Sequence Analysis, Structure and Function Prediction
PRINTS
ProDom home page
Protein Home
Services
SMART Main page
Table of Standard Genetic Code
TreeFam
UCL OWL BLAST Server
UniProt The Universal Protein Resource EBI
UniProt
UniProtKB
Virtual Ribosome
Welcome to PIR [Protein Information Resource]
http–www.psidev.info-

Rebase

Official REBASE Homepage

Repeat sequences

Gramene
RepeatMasker Home Page
Tandem Repeats Finder Basic Submit Page

Sequence Simulation

Reodon
David Posada’s Lab
indel-seq-gen Biological Sequence Simulation

Structure

cath Protein Structure Classification Database at UCL
Conserved Domains Database (CDD) and Resource Group
HHpred – Homology detection & structure prediction by HMM-HMM comparison
HMMSTR Server
loopp-web
M o l T a l k – computational environment in Structural Bioinformatics
ModBase Search Page
PDB-RCSB Protein Data Bank
PDBe Fold EMBL-EBI
PDBsum home page
PHYRE 0.2 Protein Fold Recognition Server
PHYRE Protein Fold Recognition Server
PredictProtein – Sequence Analysis, Structure and Function Prediction
Pôle Bioinformatique Lyonnais
scop Structural Classification of Proteins
SWISS-MODEL
vast Vector Alignment Search Tool

Online Classses/Resources

基因组科学 Genome Science – MOOC学院

Bioinformatics & Biological Computing Home

Bioinformatics and Genomics Bioinformatics @ CRG
FTP 目录 -blast-db 位于 ftp.ncbi.nih.gov
ONLINE ANALYSIS TOOLS
Online Lectures on Bioinformatics
Open MPI Open Source High Performance Computing
Public Library of Bioinformatics focus on bioinformatics
Research Computing Center
ROST虚拟学习团队
RSA-tools – tutorials – Position-specific scoring matrices

Others

免费文章抄袭检测_论文检测系统_论文比对论文发表_著作权保护_拷克
复制粘贴文本-PaperPass.Org论文通行证
相似度计算-PaperPass.Org论文通行证
差异表达基因筛选方法的比较_百度文库
基因表达数据分析

Blogs

科学网—十大算法展辉煌历史,十大问题引锦绣前程—趣味数据挖掘之十一 – 唐常杰的博文
科学网—隐马尔科夫模型 – 刘金定的博文
科学网—tangchangjie的博文
如何成为顶级生物信息学家精选 
蛋白质的序列分析流程
系统发育重建中主流算法的未来走向