To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.
VESPA calculates the frequency of each amino acid (or nucleotide) at each position (column) in an alignment for the query and background set, and selects the positions for which the most common character in the query set differs from that in the background set.
This program can be used to quickly detect amino acids that characterize differences between two groups of sequences. It compares two groups of sequences and looks for a "signature" pattern, or the set of amino acids that is conserved among each set, but differing between the sets. It will pick out those distinguishing amino acids, and calculate their frequencies in each set.
alphabet-OK ABCDEFGHIJKLMNOPQRSTUVWXYZ mutant-ABCs ZBCDEFGH-JKLMNOPQRSTVVWX**
In the above sequence alignment, the sequence names are alphabet-OK and mutant-ABCs. For the second sequence, no sequence information was available for the last two positions. The "I" in the first sequence was deleted in the second sequence. U has "mutated" to V, and A to Z. Hence the signature pattern for mutant-ABCs relative to alphabet-OK is:
signature Z.......-...........V...**, or 3/24 characters.
The periods (.) in the above signature indicate that the two sequences agree in those positions. The Z, -, and V show where the sequences disagree defining a signature for the "mutant-ABCs" sequence. The denominator for the three amino acid signature is 24, not 26, because no sequence information was available for the last two positions.
Information per position
Not checking the button gives a short output, just the signatures and frequencies of signature amino acids among the query and background sets. A checked button gives a long output with signatures AND the number of every amino acid found in every position for both alignments. These results might be useful if you have positions in your sequence sets that are 50% one amino acid, 50% another.
This option will show a web logo of the positions where your query and background alignments had a different signature. For more information about web logos, see WebLogo 3.
If you have slow results or browser time-outs, select this option to receive your results by email.
When citing VESPA, please cite Korber and Myers (1992).