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The PSI-BLAST service of MyHits is based on the NCBI PSI-BLAST (see tutorial) with some enhancements described below.

See MyHits PSI-BLAST tutorial

Differences with the NCBI
More databases All the public databases as well as the user databases are available for searching. Moreover it is allowed to change the databases between each cycle.
Start with more than a single sequence
  • a rectangular multiple sequence alignment (FASTA, ClustalW, MSF)
  • a raw sequence (minimum length is 30 residues)
  • a protein identifier from one myHits database, e.g. sw:THIO_ECOLI
  • a sub-sequence from a protein identifier, e.g. sw:VAV_HUMAN/1-120
Grouping of results by similarity The results are grouped according to their percent identity. The user can select a custom percentage.
Propagating the features We offer an option to the user for propagating its own feature table or the feature table of a SwissProt entry to all matches of the PSI-BLAST.
The MSA hub From the result page, the user can select either the sequences, or the individual matches to cycle directly or to send them to the MSA hub.
The MSA hub allows the user to realign its sequences and/or to edit the multiple alignment before going for a further cycle.
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J.
Nucleic Acids Res. 1997; 25:3389-3402.