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Useful software

Sequencing Analysis Tools

NCBI Home

ExPASy/SWISS-PROT

The Institute for Genomic Research


Free Software for viewing and editing Electropherograms


Sequence Analysis

  1. Nucleotide analysis tools
    • Blast your sequence against nr in NCBI
    • Blast your sequence against all seqs in TIGR-CMR
    • Multiple sequence alignment: ClustalW in BioEdit and TreeView
    • Dot Plot: Dot or matrix plots provide an easy and powerful means of sequence analysis, useful for searching out regions of similarity in two sequences and repeats within a single sequence.
    • Having Problems in heterologous gene expression? Do A Codon Usage Analysis.
  2. Protein analysis tools
    • Blast your sequence against nr in NCBI
    • Blast your sequence against all seqs in TIGR-CMR
    • Blast your sequence against all seqs in SWISS-PROT
    • Multiple sequence alignment: ClustalW in BioEdit and TreeView
    • PSORT: Predict the Sublocalization of your protein
    • Does you protein have a Signal Peptide? Try SignalP for the presence and location of signal peptide cleavage sites in amino acid sequences.
    • Protein Motif and Secondary Structure prediction tools
      • PROSITE: which consists of biologically significant sites, can help to reliably identify to which known protein family (if any) a new sequence belongs.
      • Pfam: a large collection of multiple sequence alignments and hidden Markov models covering many common protein families.
      • SCOP: Structural classification of proteins.
  3. RNA Secondary Structure Prediction
  4. Phylogenetic Analysis



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