Available Software on the LSCF Bioinformatics Unit sequence analysis server (sura)

  • EMBOSS package for Sequence Analysis

    open in new windowComplete list of EMBOSS programs
    Web access to EMBOSS open in new windowhere

  • BLAST package for Database Similarity Searches
    On command line write:
    % blastall -p program name -i query sequence -d database -o output file and press 'Enter'
    for example:
    % blastall -p blastp -i pep -d uniprot -o pep.out and press 'Enter'

    For list of the BLAST programs open in new windowclick here

  • FASTA package for Database Similarity Searches and Sequence Alignment
    On command line write:
    % FASTA program name and press 'Enter'

    open in new windowComplete list of FASTA programs

  • BLAT is an alignment tool like BLAST, but it is structured differently. Blat of DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more.
    open in new windowBLAT command line options
  • CD-hit a fast program for clustering and comparing large sets of protein or nucleotide sequences

    open in new windowCD-hit Users Guide

  • CLUSTALW program for global Multiple Alignment of Proteins or DNA sequences
    Note: Both programs are available for PC/Mac too
  • T-Coffee Omega

    T-Coffee is a multiple sequence alignment package for Proteins or DNA sequences.

    for more details about t_coffee various programs open in new windowclick here


    is a program for multiple sequence comparison by log-expectation.

    To run on sure:
    % muscle and press 'Enter'

  • MEME Motif-based sequence analysis tools
    For overview of the MEME package click open in new windowhere
  • PHYLIP software package for Inferring Phylogenies

    open in new windowComplete list of available programs


    profile HMM (hidden Markov models) methods for sensitive database searches using multiple sequence alignments as queries.

    HMMER ver 3b1 userguide in pdf is available PDF open in new windowHere