Protein level predictions 2 - Sequence alignment methods

This subset contains tools to be used for multiple sequence alignments (MSA) of proteins. Important applications of sequence alignments include secondary and tertiary structure prediction and functional prediction which  belong to the set of prediction tools we are interested in.  Accurate MSAs are a necessity for these tools to work. To obtain a perspective of recent trends of MSA's see article by Kemena and Notredame.

Programs available

• M-Coffee(T*)
• MAFFT
• MISTRAL
• PROBCONS (C*)
• PROMALS (T*)
• ClustalW2
• MUSCLE

An extensive overview of tools predicting protein level changes can be found from the recent review  article by Thusberg and Vihinen.  Click here to return to the main page of protein prediction tools.

*Categorisation according to Kemena and Notredame to C (consistency based) and T (template based) methods

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Description of programs

M-Coffee

website: M-Coffee

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Reference: Wallace et al. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res, 2006, 34, 6, 1692-1699. doi:10.1093/nar/gkl091

MAFFT

website: MAFFT

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References:

• Katoh et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 2002, 30, 14, 3059-3066. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12136088
  

• Katoh et al. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. ,2005, 33, 2, 511-518. doi:10.1093/nar/gki198

MISTRAL

"MISTRAL (Multiple STRuctural ALignment) is a novel strategy for multiple protein alignment based on the minimization of an energy function over the low-dimensional space of the relative rotations and translations of the molecules. The energy minimization avoids combinatorial searches and returns pairwise alignment scores for which a reliable a priori statistical significance can be given" (citation from Micheletti and Orland).

website:  MISTRAL

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References: Micheletti and Orland. MISTRAL: a tool for energy-based multiple structural alignment of proteins. Bioinformatics, 2009, 25, 20, 2663-2669. doi:10.1093/bioinformatics/btp506

PROBCONS

website: PROBCONS

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Reference: Do et al. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 2005, 15, 2, 330-340. doi:10.1101/gr.2821705

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PROMALS

website: PROMALS

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Reference: Pei et al. PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res., 2007, 35, Web Server issue, W649-52. doi:10.1093/nar/gkm227

ClustalW2

website: CLUSTALW2

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Reference: Larkin et al. Clustal W and Clustal X version 2.0. Bioinformatics, 2007, 23, 21, 2947-2948. doi:10.1093/bioinformatics/btm404

MUSCLE

website: MUSCLE

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Reference: Edgar. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 2004, 5, 113. doi:10.1186/1471-2105-5-113

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Useful databases

• PDB (database of protein structures containing currently around 60 000 protein structures)

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Review articles

• Kemena and Notredame. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics, 2009, 25, 19, 2455-2465. doi:10.1093/bioinformatics/btp452
• Janita Thusberg and Mauno Vihinen. Pathogenic or Not? And If So, Then How? Studying the Effects of Missense Mutations Using Bioinformatics Methods. Hum Mutat. 2009 May;30(5):703-14: doi:10.1002/humu.20938

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Other articles

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Useful Links

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