Wikiomics:Multiple sequence alignment

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See also Wikiomics:Bioinfo_tutorial#Protein_Alignment

Multiple sequence alignment is widely used in the sequence analysis. It is more reliable, and hosts more information than derived from BLAST multiple pairwise alignment. The MSA allows for identification of common regions between proteins (including motifs), finding conserved residues and analysis of evolutionary relationships between sequences.


Software producing the multiple sequence alignment

  • Clustal [1]
  • T-Coffee
  • Probcons [2]
  • Muscle [3]
  • MAFFT [4]
  • Kalign [5]
  • PCMA [6]
  • TBA
  • MultiSeq [7]

Analysis of conservation in the multiple sequence alignment

  • AL2CO

Databases of multiple sequence alignments

  • PFAM
  • InterPro
  • CDD


  1. Thompson JD, Higgins DG, and Gibson TJ. . pmid:7984417. PubMed HubMed [clustalw]
  2. Do CB, Mahabhashyam MS, Brudno M, and Batzoglou S. . pmid:15687296. PubMed HubMed [probcons]
  3. Edgar RC. . pmid:15034147. PubMed HubMed [muscle]
  4. Katoh K, Kuma K, Toh H, and Miyata T. . pmid:15661851. PubMed HubMed [mafft]
  5. Lassmann T and Sonnhammer EL. . pmid:16343337. PubMed HubMed [kalign]
  6. Pei J, Sadreyev R, and Grishin NV. . pmid:12584134. PubMed HubMed [pcma]
  7. Roberts E, Eargle J, Wright D, and Luthey-Schulten Z. . pmid:16914055. PubMed HubMed [multiseq]
  8. Pei J and Grishin NV. . pmid:11524371. PubMed HubMed [al2co]
All Medline abstracts: PubMed HubMed
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