常用生物信息学软件课件.pptVIP

常用生物信息学软件及在线分析 文奇根 2008-1-13 EMBOSS EMBOSS (The European Molecular Biology Open Software Suite) all the common sequence formats, such as EMBL, Genbank, Fasta, SwissProt, PIR, GCG, MSF, Clustal and raw can be read and written. Applied area Sequence Alignment Rapid database searching with sequence patterns Protein motif identification, including domain analysis Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats Codon usage analysis for small genomes Rapid identification of sequence patterns in large scale sequence sets Presentation tools for publication On line Resource /index.html /apps/emboss.html /pub/EMBOSS/ /download/#EMBASSY EMBOSS中的软件包按照功能的分类： grouped?by?function ◎ALIGNMENT?????⊙CONSENSUS?????⊙DIFFERENCES?????⊙DOT?PLOTS?????⊙GLOBAL?????⊙LOCAL?????⊙MULTIPLE?◎DISPLAY?◎EDIT?◎ENZYME?KINETICS?◎FEATURE?TABLES?◎INFORMATION?◎NUCLEIC?????⊙2D?STRUCTURE?????⊙CODON?USAGE?????⊙COMPOSITION?????⊙CPG?ISLANDS?????⊙GENE?FINDING?????⊙MOTIFS?????⊙MUTATION????? ⊙PRIMERS?????⊙PROFILES?????⊙REPEATS?????⊙RESTRICTION?????⊙TRANSCRIPTION?◎TRANSLATION?◎PHYLOGENY?◎PROTEIN?????⊙2D?STRUCTURE?????⊙3D?STRUCTURE?????⊙COMPOSITION?????⊙MOTIFS?????⊙MUTATION?????⊙PROFILES?◎UTILS?????⊙DATABASE?CREATION?????⊙DATABASE?INDEXING?????⊙MISC? JEMBOSS简介 JEMBOSS是在EMBOSS基础上开发出的一个有图形界面的EMBOSS平台！就是说原来的所有命令都是在命令行上键入(像DOS),现在有一些好心人做了个图形界面，你用鼠标点点就可以完成许多事情！开发语言是JAVA!We?are?developing?a?graphical?user?interface?(这就是传说中的GUI,图形用户界面)for?EMBOSS,?written?in?Java?and?called?Jemboss.?It?will?be?compatible?with?all?future?releases?of?EMBOSS?and?be?part?of?the?EMBOSS?distribution.?It?assists?in?the?setup?of?the?files?for?input?into?the?EMBOSS?applications?to?be?run?and?keep?a?record?of?the?results?produced.?You?will?be?able?to?run?Jemboss?in?two?different?ways.?The?first?is?as?a?standard?graphical?interface?to?EMBOSS?that?runs?on?a?Unix?server,?so?that?users?with?X-windows?can?run?it?on?the?HGMP?servers?(or?local?servers)?and?view?the?outp