probcons1

Usage

Overview

probcons is a tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN.

probcons aligns sequences provided in MFA format. This format consists of multiple sequences. Each sequence in MFA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (“>”) symbol in the first column.

Options

-clustalw

use CLUSTALW output format instead of MFA

-c --consistency REPS

use 0 <= REPS <= 5 (default: 2) passes of consistency transformation

-ir --iterative-refinement REPS

use 0 <= REPS <=1000 (default: 100) passes of iterative-refinement

-pre --pre-training REPS

use 0 <= REPS <= 20 (default: 0) rounds of pretraining

-pairs

generate all-pairs pairwise alignments

-viterbi

use Viterbi algorithm to generate all pairs (automatically enables -pairs)

-v --verbose

Report progress while aligning (default: off)

-annot FILENAME

write annotation for multiple alignment to FILENAME

-t --train FILENAME

compute EM transition probabilities, store in FILENAME (default: no training)

-e --emissions

also reestimate emission probabilities (default: off)

-p --paramfile FILENAME

read parameters from FILENAME (default: )

-a --alignment-order

print sequences in alignment order rather than input order (default: off)

Reference

Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.