Good multiple alignments tools are required for the generation of better motif descriptors (pat, prf, hmm). However these tools are computer intensive, try to limit yourself...
Tips: ClustalW is faster than T-Coffee, but T-Coffee is more accurate, especially when sequences share less than 30% identity. MAFFT is much faster than ClustalW and T-Coffee and very accurate.
Tips: ClustalW is faster than T-Coffee, but T-Coffee is more accurate, especially when sequences share less than 30% identity. MAFFT is much faster than ClustalW and T-Coffee and very accurate.
| Input | You must paste at least 3 sequences (or identifiers). The limitations, on the upper number of sequences (or identifiers) and the total number of residues allowed, may vary according to the current hardware availability. |
| Sequence format |
The input sequences must be in FASTA (Pearson) format. Example: (cut&paste in the tool text area) >seqA GARFIELDTHEFASTCAT >seqB GARFIELDTHEVERYFASTCAT >seqC GARFIELDTHEFATCAT |
| Sequence names | Each sequence must have a different name (8 first characters are significants). |
| Other | Avoid special characters, e.g. +"*%&/()!?'@€<>,;:$=| |
ClustalW
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson JD, Higgins DG, Gibson TJ.
Nucleic Acids Res. 1994 Nov; 22(22):4673-80.
T-Coffee
T-Coffee: A novel method for multiple sequence alignments
C. Notredame, D. Higgins, J. Heringa
Journal of Molecular Biology 2000 Sept; 302(1):205-217.
MAFFT
Improvement in the accuracy of multiple sequence alignment program MAFFT.
K. Katoh, K. Kuma, T. Miyata and H. Toh
Genome Informatics. 2005; 16(1):22-33.
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
K. Katoh, K. Kuma, H. Toh and T. Miyata
Nucleic Acids Res. 2005; 33:511-518.
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
K. Katoh, K. Misawa, K. Kuma and T. Miyata
Nucleic Acids Res. 2002; 30:3059-3066.
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson JD, Higgins DG, Gibson TJ.
Nucleic Acids Res. 1994 Nov; 22(22):4673-80.
T-Coffee
T-Coffee: A novel method for multiple sequence alignments
C. Notredame, D. Higgins, J. Heringa
Journal of Molecular Biology 2000 Sept; 302(1):205-217.
MAFFT
Improvement in the accuracy of multiple sequence alignment program MAFFT.
K. Katoh, K. Kuma, T. Miyata and H. Toh
Genome Informatics. 2005; 16(1):22-33.
MAFFT version 5: improvement in accuracy of multiple sequence alignment.
K. Katoh, K. Kuma, H. Toh and T. Miyata
Nucleic Acids Res. 2005; 33:511-518.
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
K. Katoh, K. Misawa, K. Kuma and T. Miyata
Nucleic Acids Res. 2002; 30:3059-3066.