Sequence analysis softwares

• sequence data retrieval

• Entrez - a molecular biology database and retrieval system, developed by the National Center for Biotechnology Information (NCBI), provides access to DNA and protein sequence databases, 3D structures database, genomes and maps databases and the literature (PubMed). The taxonomy database contains more than 23 000 different species and allows retrieval of DNA and protein sequences for any taxonomic groups.
• SRS - a homogeneous interface to over 80 biological databases, developed at the European Bioinformatics Institute (EBI) at Hinxton, UK. The databases include those of sequence and sequence related, metabolic pathways, transcription factors, application results (e.g. BLAST), protein 3D structure, genome, mutations and locus-specific mutations.
•  DBGET/LinkDB - an integrated database retrieval system, developed by the Insitute for Chemical Research, Kyoto University and the Human Genome Center of the University of Tokyo. DBGET provides access to about 20 databases, including KEGG, the Kyoto Encyclopedia of Genes and Genomes database.

• database searching and sequence alignment

  　

  • BLAST, WuBLAST, PSI-BLAST
  • FASTA
   
  • CLUSTALW, CLUSTALX - multiple sequence alignment
   
  • profile and profile HMM
    • SAM
    • HMMER
    • HMMpro

    　

• computational gene finding

  　

  • bibliographies
  • HMM-based genefinders
    • Genie
    • GenScan
    • HMMgene
    • GENEMark-HMM
    • Veil
  • other genefinders
    • GeneParser
    • MZEF