注册 登录  
 加关注
   显示下一条  |  关闭
温馨提示!由于新浪微博认证机制调整,您的新浪微博帐号绑定已过期,请重新绑定!立即重新绑定新浪微博》  |  关闭

云之南

风声,雨声,读书声,声声入耳;家事,国事,天下事,事事关心

 
 
 

日志

 
 
关于我

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

网易考拉推荐

CSC-IT Center for Science  

2010-01-07 14:01:36|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

  下载LOFTER 我的照片书  |
http://www.csc.fi/english/research/sciences/bioscience/programs



 
Tehdyt toimenpiteet

Bioinformatics Tools

Programs marked with W can be used with a web browser.

General sequence analysis packages

  • EMBOSS  Programs for analysing DNA and amino acid sequence data. W


DNA microarray data analysis

  • Chipster Easy-to-use graphical software for DNA microarray data analysis based on R/Bioconductor

  • R / Bioconductor A statistical environment with support for genomics


Sequence assembly

  • MIRA Whole Genome Shotgun and EST Sequence Assembler
  • Velvet assembler for very short reads
  • SAMtools utilities for manging SAM/BAM formatted alignmnet files

Promoter analysis

Database searching and sequence alignment

  • BLAST Sequence database homology search tool. W

  • Exonerate  Generic sequence alignment tool W
  • HMMER Sequence database search based on profile-HMM.

  • PairsDB  A tool to retrieve pre-calculated BLAST and PSI-BLAST results form the PairsDB database. W
  • SSAHA2 Fast hash function based search tool for DNA sequences
  • Wise2 (GeneWise) comparing protein sequences and HMMs to nucleotide sequences

Multiple sequence alignment

  • CD-HIT Sequence clustering and redundancy removal
  • ClustalW Multiple sequence alignment W

  • Muscle A fast and accurate multiple sequence alignment program W
  • MAFFT Multiple sequece alignment program W
  • Seaview A multiple sequence alignment editor

  • JalView A multiple sequence alignment editor

Pathway analysis

Phylogenetics

  • MrBayes Program for inferring phylogenies using bayesian methods
  • PHYLIP Package for inferring phylogenies W

  • POY Program for inferring phylogenies

  • RAxML Fast program for inferring phylogenies with likelihood

  • TNT A fast program for inferring phylogenies with parsimony methods

Structural Biology

  • Discovery Studio Molecular modeling package D
  • Maestro Molecular modeling package

  • RasMol Molecular graphics visualisation

  • Rosetta Protein structure prediction and protien docking tool
  • VMD Molecular graphics visualisation

RNA secundary structure prediction

  • Vienna Package (within EMBOSS)

Gene mapping

  • MERLIN A fast program for nonparametric linkage, and haplotyping

  • LINKAGE / FASTLINK Parametric linkage analysis

  • GENEHUNTER Multi-point linkage calculations for small pedigrees

  • SNPHAP Population-based SNP haplotype reconstruction

  • SimWalk2 Haplotyping, and non-parametric analysis

  • DHSMAP Fine-mapping of qualitative traits by linkage disequilibrium

  • SLINK Power simulation tool for linkage studies based

  • PedCheck Detects marker typing incompatibilities in pedigree data

  • Mega2 Converts Linkage-format files to other formats

  • Pseudomarker Joint linkage and LD analysis

Systems biology

  • bestim Gene regulatory network inference under the Boolean network model.

  • decomptool Decomposition of biochemical networks into subnetworks

  • FBAtool A program for flux balance analysis of metabolic networks

  • SOSlib Program for running simulations for SBML formatted models.

Other tools

  • Bioperl Bioinformatics tools for perl programming

  • Jnet Protein secondary structure prediction program

  • Primer PCR primer design

  • TMHMM Transmembrane helix prediction tool


CSC logo
CSC — IT Center for Science Ltd. About the site ? CSC
 
  评论这张
 
阅读(579)| 评论(0)
推荐 转载

历史上的今天

在LOFTER的更多文章

评论

<#--最新日志,群博日志--> <#--推荐日志--> <#--引用记录--> <#--博主推荐--> <#--随机阅读--> <#--首页推荐--> <#--历史上的今天--> <#--被推荐日志--> <#--上一篇,下一篇--> <#-- 热度 --> <#-- 网易新闻广告 --> <#--右边模块结构--> <#--评论模块结构--> <#--引用模块结构--> <#--博主发起的投票-->
 
 
 
 
 
 
 
 
 
 
 
 
 
 

页脚

网易公司版权所有 ©1997-2016