A tool to extract sequences matching a given region of
AF009606 reference genome.
The region to be searched could be defined with a from/to or by a sequence pasted in the right box.
The length of matching sequences extracted is defined by length of the query sequence +/- a precentage set by the user.
A multiple sequence alignment is computed if not too many and too long similar sequences are found. For this alignment, all identical sequences are removed.
If the alignment has been computed, a repertoire and Shannon entropies are computed too. For repertoire a parameter allow the user to hide residue with a frequency below this parameter.
The default sequence databank searched contains all the euHCVdb sequences (nucleotides or proteins). The user could upload its own sequence databank. The latter is then used for the similarity search. The sequence databank could be the result of a request on the database.
N.B.:This tool is sequence based i.e. it extracts sequences by using a similiratity search program.
It is less accurate than querying the database, but this is correctyed by the possibility to upload a sequence databank.
However it allows the extraction of sequence spanning several genomic regions or proteins or sub-genomic or sub-protein regions in one step.
© - Comments - Funded by HepCVax (EC # QLK2-CT-2002-01329) and VIRGIL (EC # LSHM-CT-2004-503359) - Developped by the EBRS/IBCP/UMR5086/CNRS/UCBL