The query sequence must be a amino acid sequence. At present, SALSA will not accept nucleotide query sequences. Entering a nucleotide query sequence will give silly results. The query sequence may be in plain text format, or in FASTA, SWISS-PROT, GenPept or PIR format, in which case a sequence description may be included which will be shown in the output. You may use SRS or Entrez to retrieve your query sequence, and then copy and paste the sequence into the text area. All characters that are not in the set of legal amino acid residue symbols (ABCDEFGHIKLMNPQRSTVWXYZ) in upper or lower case will be removed and ignored. The maximum length of the query sequence is 2000 amino acids.
You can choose from a wide range of sequence databases, containing both amino acid and nucleotide sequences. In addition to general databases like SWISS-PROT and the non-redundant sequence databases from NCBI, a number of more or less finished genome databases are available. Note that some of the sequence data that is available for searching using this service may be incomplete and may contain errors. In particular, some of the genome sequence data is far from finished and has not been submitted to the general databases (GenBank/EMBL/DDBJ). The non-redundant and EST databases are updated once a week with data from NCBI. The weekly database is updated every night. When searching a nucleotide sequence database, SALSA will translate each database sequence in all six possible frames using the standard genetic code and compare them individually to the amino acid query sequence.
The sensitivity, speed and other aspects of the search can be controlled by adjusting the search options. However, for most searches, they can be left at their default values.
The list of matching sequences will show a description of the sequence, the estimated score, the score of the best fragment (ungapped), and the expected number of random hit with that score. If "SW for E<100" is enabled the optimal score will also be shown, and the expect value will be calculated from the optimal score. The initial part of the sequence description is linked to the full sequence entry in Entrez. Sequence alignments are shown below the hit list.
Copyright © 1999 Torbjørn Rognes. Last updated 1999-01-18.