Gene Cutter

Sequence Alignment and Protein Extraction

Purpose: Gene Cutter is a sequence alignment and protein extraction tool for HIV-1, HIV-2 or SIV. This tool will:

• Align your nucleotide sequences (if they aren't already aligned).
• Clip coding regions from a nucleotide alignment.
• Codon-align all coding regions.
• Generate nucleotide and protein alignments of the cut regions.

Please read Gene Cutter Help, particularly before running large jobs.

Organism	HIV1 (HXB2) HIV2 (SMM239) SIV (SMM239)
Paste your sequences [Sample Input]
Or upload your file
Check if appropriate	Sequences are unaligned

Region(s) to align and extract	All genes and complete sequence Complete sequence Gag-Pol Gag p17 (matrix) p24 (capsid) p2 p7 (nucleocapsid) p1 p6 Pol CDS protease p51 (RT) p15 (RNase) p31 (integrase) Vif CDS Vpr CDS Tat CDS (includes intron) Tat exon 1 Tat exon 2 Rev CDS (includes intron) Rev exon 1 Rev exon 2 Vpu CDS Env CDS V1 V2 V3 V4 V5 RRE gp41 gp120 Nef CDS
Reference options	Insert HXB2(K03455) for HIV-1 or SMM239(M33262) for HIV-2/SIV into the results
	Remove HXB2(K03455) for HIV-1 or SMM239(M33262) for HIV-2/SIV from the results
Check if appropriate	Codon align the region
Output format	Translate to amino acids: Codons containing an IUPAC character shown as "X" Codons containing an IUPAC character in a silent position translated; others shown as "X" Codons containing an IUPAC character translated Return results as nucleotides: Do not translate