HCV Sequence Alignments
- The web alignments have been manually optimized, and contain only
one sequence from one patient. Please note that for most genes, only sequences
that cover the entire gene are included. Exceptions are both UTRs
and the complete genome, where this rule would result in the loss of too
many sequences. Very similar or epidemiologically related groups have also
been reduced to one sequence, with the exception of the 5' UTR where sequences
that are nearly identical but almost certainly not epidemiologically related
were not removed; this region is so conserved that few sequences would have
remained. Sequences that are not genotyped are also not included, but sequences
that have a genotype but no subtype are; however, no consensus sequences were
made for these.
- The reference alignments contain approximately 4 representatives of
each clade, and are useful for classifying new sequences.
- The consensus sequences are only available for genotypes for which
the alignment contains at least three sequences. The original sequences
are also included in the consensus sequence files. The consensus sequences
consist of upper- and lower case letters; the lowercase indicates that
the consensus is not unanimous. Please note that the parameters used to
generate these consensus sequences are set so that gaps are avoided where
possible; i.e., if a consensus is based on 50 sequences of which 49 have a
gap but one has a valid residue code, the consensus will contain that code.
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Questions or comments? Contact us at
hcv-info@lanl.gov