Wikiomics:Multiple sequence alignment

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(added tags)
Line 35: Line 35:
#multiseq pmid=16914055
#multiseq pmid=16914055
</biblio>
</biblio>
 +
 +
 +
[[Category:Protocol]]
 +
[[Category:In silico]]
 +
[[Category:Sequence analysis]]

Revision as of 15:47, 3 March 2008

Template:Text-needed


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.

Contents

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

References

  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
Personal tools