HCV Database
HCV sequence database
 



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.


Consensus Maker

Purpose: To calculate consensus sequences. We provide three tools for generating a consensus of your alignment.

Type Description Example
Simple Computes a consensus using customary parameters. Try this first to see if it meets your needs.
CON          Acg-?TTAG
sequence1    ACGTATTAG
sequence2    ACG-AT---
sequence3    ACT-CT---
sequence4    ATT-CX---
sequence5    ACG-AT---
sequence6    ACG-CT---
sequence7    ACG-TT---
         
Advanced

Allows greater control over consensus parameters. User can adjust values for majority and unanimous, specify which characters to consider, choose how to handle gaps, etc. Multiple consensuses can be made for consensus blocks (blocks of sequences within a single alignment), such as the "B" and "G" blocks in the example at right. A consensus of consensuses can be made.

Help file: Advanced Consensus Maker Explanation

CON_OF_CONS     ACG-?TTAG
CON_B           Acg-?TTAG
B.sequence1     ACGTAtTAG
B.sequence2     ACG-AT---
B.sequence3     ACT-CT---
B.sequence4     ATT-CX---
CON_G           ACG-?T???
G.sequence1     ACG-AT---
G.sequence2     ACG-CT---
G.sequence3     ACG-TT---   
Ambiguity

Produces a consensus that includes IUPAC ambiguity codes. Consensus blocks supported. Nucleotide alignments only.

Help file: Ambiguity Consensus Maker Explanation

CON_B           AYKTMTTAG
B.sequence1     ACGTATTAG
B.sequence2     ACG-AT---
B.sequence3     ACT-CT---
B.sequence4     ATT-CX---
CON_G           ACG?HT???
G.sequence1     ACG-AT---
G.sequence2     ACG-CT---
G.sequence3     ACG-TT---   





Questions or comments? Contact us at hcv-info@lanl.gov