Ambiguity Consensus Explanation
Ambiguity Consensus Maker takes an input file of aligned nucleotide sequences in most standard formats and calculates a consensus sequence made up of the IUPAC ambiguity codes for each column in the alignment. The consensus alone may be returned by the program or the user has the option to append the original alignment to the consensus. A copy of the output file may be downloaded. 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; it does not create 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 in this program is to click the blue Sample Input button at the top of the submission page. This causes a simple, hypothetical alignment (in table format) to be loaded into the form. You can then calculate the consensus of this alignment under varying input options to see the results of those options. Each column of the Sample Input has been chosen to illustrate the IUPAC codes.
Input file options
- Format of input alignment. Consensus Maker recognizes most standard alignment formats. If the program fails to decipher your format try resubmitting the alignment in fasta or table format.
- Squeeze gaps. If your alignment contains columns that are entirely gaps they will be removed before a consensus is calculated. Default = squeeze gaps. You can also specify what character is used in your alignment to signify gaps. The default is "-".
Note, if your alignment contains sequences of varying length, Consensus Maker will equalize the lengths of sequences by adding spaces to the ends of short sequences.
Consensus output options
- Do consensus for each block. If the input contains blocks of sequences then calculate a consensus for each block, not just a single consensus for the alignment as a whole. Default = false. If false only a single consensus is computed for the entire alignment. If true then you must insure that the names of the sequences in your alignment follow a conventional format that can be read by the program. Sequences must have names like "A.US.57866" . The program reads the letter(s) before the first dot ("A") and uses it to define an "A" group of sequences. Another group of sequences will be defined in the alignment if that first character changes, e.g., B.FR.98332. Example. This naming convention is that followed by the HIV database. The output will have a CONSENSUS_A and a CONSENSUS_B. If more than one character is present before the first dot those characters will become the block name; e.g., CRF01AE.X34577 will define a CRF01AE consensus block. If you don't want to calculate multiple consensuses then your sequences can be named however you like.
- Min. no. seqs. for consensus. If a block contains fewer than "n" sequences, then don't calculate a consensus for that block. Default = 3. This number only applies to blocks within an alignment.
- Consensus + alignment. Results will show consensus appended to the top of the user's alignment. Default = true. When false, the output consists of the consensus alone.
- Show number of sequences. If consensuses are to be computed for each block in the alignment this option will show how many sequences occurred in each block. The number will be shown following each consensus name, e.g., CON_A(23). The default is to not show numbers.
Consensus calculation options
- Characters to count when making consensus. The program considers "ACGTU" when making a consensus. Don't mix "U" and "T" in the same alignment.
- Character presence percentage. If a column of an alignment contained 99 "A" and 1 "G" would you want to give this a consensus of "A" or "R", where "R" is the IUPAC code for "purine" (A and G are purines). In other words if a character is present below a certain "presence percentage" threshold should it be ignored when making the consensus. You can set this presence percentage threshold in the box provided. The default is "0" which means every occurrence of an A,C,G,T, or U counts. If you had set the value to, say 2%, then the G in the above example would be ignored and the consensus would be "A".
Examples
Example of using names to identify alignment blocks:
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
Example of "pretty print" output:
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
Example of "output aligned" output:
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 ---------- ---------- ---------- ---------- ----------
Example of formatted output (nexus):
#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;
