MyHits has reached its end of life and no longer provides data or services. Thank you for your support and trust for more than 23 years!
However, the webserver will remain online in its present form at least until end of March 2025.
To ensure the future of MyHits, we would be happy if a person or community would take over the resource or parts of it. Interested? Please contact us (myhits [at] sib.swiss).
Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Hau J, Martin O, Kuznetsov D, Falquet L.
MyHits: improvements to an interactive resource for analyzing protein sequences.
Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W433-7
However, the webserver will remain online in its present form at least until end of March 2025.
To ensure the future of MyHits, we would be happy if a person or community would take over the resource or parts of it. Interested? Please contact us (myhits [at] sib.swiss).
Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Hau J, Martin O, Kuznetsov D, Falquet L.
MyHits: improvements to an interactive resource for analyzing protein sequences.
Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W433-7
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.