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 takes an input file of aligned DNA or protein sequences in most standard formats and calculates a consensus sequence. You have the option to download the consensus alone, or to prepend the consensus to the original alignment. If the input alignment comprises blocks of sequences (e.g., HIV sequences grouped by subtype), then the program can calculate a consensus for each sequence block and a consensus of the consensuses. The program recognizes sequence blocks by how the component sequences are named.
A good way to understand the options available is to click the Sample Input button on the submission page. This loads a simple, hypothetical alignment (in table format) into the form:
A.seq1 A-CGTATTAG A.seq2 A-CG-AT--- A.seq3 A-CT-CT--- A.seq4 A-TT-CX--- B.seq1 A-CG-AT--- B.seq2 A-CG-CT--- B.seq3 A-CG-TT---
You can then calculate the consensus of this alignment under varying options to see the results of those options. Each column of the Sample Input has been chosen to illustrate the effect of the various options. Using default options, the output looks like:
CON_OF_CONS ACG-?T--- CON_A Acg-?T--- A.seq1 ACGTATTAG A.seq2 ACG-AT--- A.seq3 ACT-CT--- A.seq4 ATT-CX--- CON_B ACG-?T--- B.seq1 ACG-AT--- B.seq2 ACG-CT--- B.seq3 ACG-TT---Col. 1: unanimity, Col. 2: all gaps, column squeezed, Col. 3: majority, Col. 4: no majority letter but resolvable by common character, Col. 5: gaps, Col. 6: irresolvable tie in consensus, Col. 7: undefined character, Cols. 8-10: missing information (trailing blanks).
CON A-CG-?TTAG A.seq1 A-CGTATTAG A.seq2 A-CG-AT--- A.seq3 A-CT-CT--- A.seq4 A-TT-CX--- B.seq1 A-CG-AT--- B.seq2 A-CG-CT--- B.seq3 A-CG-TT---
In the table-formatted file below there are two blocks, an "A1" block and a "B" block recognizable by the "A1." and "B." (note the dot) with which the names begin. Two consensuses will be calculated for this alignment if "Do consensus for each block" is true and "Min. no. seqs. for consensus" is 3.
A1.FR.83.IIIB_A04321 aaactatcgtagctagctagctgatcgatgctagctgatcg.... etc A1.FR.83.IIIC_A04322 aaactatcgtagctagctag------gatgctagctgatcg.... etc A1.DE.96.POIURR_A04322 aaactatcgtagctagctag------gatgctagctgatcg.... etc B.FR.82.LAI_K03455 aaactatcgtagctagctttctgatcgatgctagctgatcg.... etc B._._.N833_AF76511 acactatcgtagctagctagctgatcgatgctagctgatcg.... etc B.US.99.JK77_AF76511 acactatcgtagctagctagctgatcgatgctagctgatcg.... etc
CON gccagccccc tgaTGGGGGC GACaCTCCAC CATGAATCAC tCCCCTGTGA 1a.-.COLONEL_AF290978 ---------- --TTGGGGGC GACACTCCAC CATGAATCAC CCCCCTGTGA 1a.-.H77_AF009606 GCCAGCCCCC TGATGGGGGC GACACTCCAC CATGAATCAC TCCCCTGTGA 1a.-.HEC278830_AJ278830 GCCAGCCCCC TGATGGGGGC GACGCTCCAC CATGAATCAC TCCCCTGTGA CON GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCaTGGCG TTAGTATGAG 1a.-.COLONEL_AF290978 GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG 1a.-.H77_AF009606 GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG 1a.-.HEC278830_AJ278830 GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCGTGGCG TTAGTATGAG CON TGTCGTGCAG CCTcCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG 1a.-.COLONEL_AF290978 TGTCGTGCAG CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG 1a.-.H77_AF009606 TGTCGTGCAG CCTTCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG 1a.-.HEC278830_AJ278830 TGTCGTGCAG CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG
CON gccagccccc tgaTGGGGGC GACaCTCCAC CATGAATCAC tCCCCTGTGA 1a.-.COLONEL_AF290978 .......... ..T------- ---------- ---------- C--------- 1a.-.H77_AF009606 ---------- ---------- ---------- ---------- ---------- 1a.-.HEC278830_AJ278830 ---------- ---------- ---G------ ---------- ---------- CON GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCaTGGCG TTAGTATGAG 1a.-.COLONEL_AF290978 ---------- ---------- ---------- ---------- ---------- 1a.-.H77_AF009606 ---------- ---------- ---------- ---------- ---------- 1a.-.HEC278830_AJ278830 ---------- ---------- ---------- ----G----- ---------- CON TGTCGTGCAG CCTcCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG 1a.-.COLONEL_AF290978 ---------- ---------- ---------- ---------- ---------- 1a.-.H77_AF009606 ---------- ---T------ ---------- ---------- ---------- 1a.-.HEC278830_AJ278830 ---------- ---------- ---------- ---------- ----------
#NEXUS begin taxa; dimensions ntax=4; taxlabels CON 1a._.COLONEL_AF290978 1a._.H77_AF009606 1a._.HEC278830_AJ278830 ; end; begin characters; dimensions nchar=150; format interleave datatype=dna; matrix CON gccagccccctgaTGGGGGCGACaCTCCACCATGAATCACtCCCCTGTGA 1a._.COLONEL_AF290978 ------------TTGGGGGCGACACTCCACCATGAATCACCCCCCTGTGA 1a._.H77_AF009606 GCCAGCCCCCTGATGGGGGCGACACTCCACCATGAATCACTCCCCTGTGA 1a._.HEC278830_AJ278830 GCCAGCCCCCTGATGGGGGCGACGCTCCACCATGAATCACTCCCCTGTGA CON GGAACTACTGTCTTCACGCAGAAAGCGTCTAGCCaTGGCGTTAGTATGAG 1a._.COLONEL_AF290978 GGAACTACTGTCTTCACGCAGAAAGCGTCTAGCCATGGCGTTAGTATGAG 1a._.H77_AF009606 GGAACTACTGTCTTCACGCAGAAAGCGTCTAGCCATGGCGTTAGTATGAG 1a._.HEC278830_AJ278830 GGAACTACTGTCTTCACGCAGAAAGCGTCTAGCCGTGGCGTTAGTATGAG CON TGTCGTGCAGCCTcCAGGACCCCCCCTCCCGGGAGAGCCATAGTGGTCTG 1a._.COLONEL_AF290978 TGTCGTGCAGCCTCCAGGACCCCCCCTCCCGGGAGAGCCATAGTGGTCTG 1a._.H77_AF009606 TGTCGTGCAGCCTTCAGGACCCCCCCTCCCGGGAGAGCCATAGTGGTCTG 1a._.HEC278830_AJ278830 TGTCGTGCAGCCTCCAGGACCCCCCCTCCCGGGAGAGCCATAGTGGTCTG ; end;