Protein Sequence Tools

  • AASTATS - Statistics Based on Amino Acid Abundance (replaced by PEPINFO)
  • ALIGN - Optimal Global Alignment of Two PS
  • BL2SEQ - Compare proteins to each other with BLAST
  • BL2SEQX Compare a protein to a nucleotide sequence with BLAST, use BL2SEQ
  • BLASTP - Compare a PS to a PS DB
  • BLIMPS - Sequence Search Against BLOCKS Profiles
  • CHOFAS - Predict Secondary Stucture of PS(s) (replaced by PROTEUS)
  • CLUSTALW - Multiple Sequence Alignment
  • CLUSTALWPROF - Align Sequences to Existing Alignment (Profile)
  • DEGAPSEQ - Remove Gaps from Sequences
  • EXTCOEF - Extinction coefficient calculation (replaced by PEPSTATS)
  • FASTA - Heuristic Sequence Similarity Search (PS Or DB)
  • FingerPRINTScan - PRINTS fingerprint identification
  • GOR4 - Predict Secondary Structure of PS (replaced by PROTEUS)
  • GREASE - Kyte-Doolittle Hydropathy Profile (replaced by PEPWINDOW).
  • HMMPFAM - Search against Pfam HMM database
  • HELIXTURNHELIX (HTH) - Predict HTH Motifs in Protein Chains
  • LALIGN - Calculate N-Best Local PS Alignments
  • MSA - Multiple Sequence Alignment (Sum-of-Pairs Criterion)
  • PEPINFO - histograms of protein properties
  • PEPSTATS - extinction coefficient, PI calculation, etc.
  • PEPWINDOW - Protein hydropathy plots (Replaces Grease).
  • PFSCAN- Sequence search against a set of profiles
  • PFSEARCH - Search a PROSITE profile against a sequence database
  • PI - Isoelectric point determination (replaced by PEPSTATS)
  • PPSEARCH - Search Prosite DB for Patterns in a PS
  • PROSEARCH - Search Prosite DB for Patterns in a PS
  • PROTEUS - Protein Secondary Structure predictionnew (replaces CHOFAS, GOR4)
  • PRSS - Compare a PS to a Shuffled PS
  • PSIBLAST - Position Specific Iterative BLAST
  • RPSBLAST - Compare a PS to a Conserved Domain DB
  • SAPS - Statistical Analysis of PS (replaced by PEPSTATS)
  • SSEARCH - Smith-Waterman Local Alignment of Proteins
  • TBLASTN - Compare a PS to a translated DB
  • TFASTA - Compare a PS to a NS->PSDB
  • TFASTX - Comp PS to Trans DNA (NS Or DB)
  • TFASTY - Comp PS to Trans DNA (NS Or DB)
  • TMAP - Prediction of Transmembrane Segments
  • TMHMM - Predict location of transmembrane helices and location of intervening loop regions

If you don't see the tool you need, please Let us know! We can add tools very quickly.