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SequenceAnalysisTools生物信息学.ppt

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Sequence Analysis Tools Introduction Introduction of sequence analysis tools Different analysis tools Standard Unix tools (e.g., the grep family, sed, awk, and cut). Publicly available tools (e.g., BLAST, the EMBOSS package,DNAstar, vector NTI). Open source libaries (e.g., BioPerl, BioJava, BioPython, BioRuby). Custom tools. The field of sequence analysis Many of the software tools used in studying sequence analysis, which is one of the many subfields of computational molecular biology. The field of sequence analysis includes Primer Design Pattern and motif searching Sequence comparison Multiple sequence alignment Sequence composition determination Secondary structure and 3D prediction Phylogenetic analysis Readseq Readseq is a classic sequence format convert tools. 1989. Developed by Don Gilbert, Function:this program reads and writes nucleotide and protein sequences in many useful formats. To run Readseq use: java -cp readseq.jar run options inputfiles Supported formats: GCG,fasta,genbank embl,msf… Primer Design Oligo 6 (引物评价)* Premier Primer (自动搜索)* Vector NTI Suit Dnasis Omiga Dnastar Primer3 (在线服务)* Clustal Clustal is a general-purpose multiple sequence alignment program for nucleotide sequences or proteins. Function:It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Clustal Download address ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/clustalx1.8.msw.zip Clustalw for dos Clustalx for windows Clustalv for unix or linux HMMER HMMER is a collection of programs that create a hidden Markov model (HMM) of a sequence family which can be utilized as a query against a sequence database to identify (and/or align) additional homologs of the sequence family. HMMER was developed by Sean Eddy at Washington University. HMMER Download address: /pub/eddy/hmmer/2.2g/hmmer-2.2g.bin.dos-cygwin.zip

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