Gene Cutter: Sequence Alignment and Protein Extraction

Purpose: Gene Cutter is a sequence alignment and protein extraction tool. It can be used for any set of nucleotide sequences for HIV-1, HIV-2 or SIV.

Gene Cutter can:

• align your nucleotide sequences (if they aren't already aligned)
• clip pre-defined coding regions from a nucleotide alignment
• codon-align the coding regions
• generate nucleotide and protein alignments of the cut regions

Details: The reference sequence used by this tool is HXB2(Accession #K03455) for HIV-1 or SMM239(Accession #M33262) for HIV-2 or SIV. Gene coordinates are based on these reference sequences. This version of Gene Cutter doesn't require a reference sequence to be included in your input nucleotide alignment. Gene Cutter will also accept unaligned sequence sets. Gene Cutter uses Hmmer with a training set of the full-length genome alignment and will give a better multiple alignment than many computationally-based alignment programs. Mis-alignments at the ends of a coding region may result in a few amino acids/bases not appearing in the output for that coding region.

In some sequences, an insertion will be compensated within a short distance by a deletion, or vice versa. As these frameshifts may not inactivate the protein, if a compensating mutation is within 5 amino acids of an initial frameshift, the shifted reading frame is left intact. Otherwise, the frame shift is marked with the hash symbol (#), and the translation is continued in the correct reading frame beyond the offending codon. Stop codons are marked by a dollar sign ($).

The best results will be obtained if you submit an alignment that has been hand-aligned and contains the correct reference sequence. For more information, see Gene Cutter Explanation.