Smith-Waterman & Needleman-Wunsch Alignment in C
url: https://github.com/noporpoise/seq-align
author: Isaac Turner turner.isaac@gmail.com
license: GPLv3
updated: 8 May 2013
C implementations of optimal local (Smith-Waterman) and global
(Needleman-Wunsch) alignment algorithms. Written to be fast, portable and easy
to use. Commandline utilities smith_waterman and needleman_wunsch provide
great flexibility. Code can also be included easily in third party programs,
see nw_example/ and sw_example/ directories for examples. Also includes perl
modules to provide perl API to programs.
Features:
- Align any pair of ASCII sequences (DNA, Protein, words, etc.)
- Specify alignment scoring systems or choose a common one (BLOSUM etc.)
- Specify wildcards that match any character with a given score
- Align with no mismatches (
--nomismatches), or no gaps (--nogaps) with local and global alignment. When both used for local alignment, lists common substrings in order of length/score - Read fastq, fasta, sam, bam, plain (one sequence per line) and gzipped files
- Display in colour (
--colour) - Show alignment context when doing local alignment (
--context <n>) - Allow a penalty free gap at the beginning or end of a global alignment
(
--freestartgapand--freeendgap) - Default behaviour is case-insensitve matching, change using
--case_sensitive
Fetch and build dependencies (requires git, make and zlib)
$ cd libs
$ make
$ cd ..
Build seq-align:
$ make
For those interested, the depedencies used are:
- htslib [https://github.com/samtools/htslib]
- bit_array [https://github.com/noporpoise/BitArray]
- string_buffer [https://github.com/noporpoise/string_buffer]
- seq_file [https://github.com/noporpoise/seq_file]
usage: ./bin/smith_waterman [OPTIONS] [seq1 seq2]
Smith-Waterman optimal local alignment (maximises score).
Takes a pair of sequences on the command line, or can read from a
file and from sequence piped in. Can read gzip files and FASTA.
OPTIONS:
--file <file> Sequence file reading with gzip support - read two
sequences at a time and align them
--files <f1> <f2> Read one sequence from each file to align at one time
--stdin Read from STDIN (same as '--file -')
--case_sensitive Use case sensitive character comparison [default: off]
--match <score> [default: 2]
--mismatch <score> [default: -2]
--gapopen <score> [default: -1]
--gapextend <score> [default: -1]
--scoring <PAM30|PAM70|BLOSUM80|BLOSUM62>
--substitution_matrix <file> see details for formatting
--substitution_pairs <file> see details for formatting
--wildcard <w> <s> Character <w> matches all characters with score <s>
--minscore <score> Minimum required score
[default: match * MAX(0.2 * length, 2)]
--maxhits <hits> Maximum number of results per alignment
[default: no limit]
--context <n> Print <n> bases of context
--printseq Print sequences before local alignments
--printfasta Print fasta header lines
--pretty Print with a descriptor line
--colour Print with colour
EXPERIMENTAL (and buggy):
--nogapsin1 No gaps allowed in the first sequence
--nogapsin2 No gaps allowed in the second sequence
--nogaps No gaps allowed in either sequence
--nomismatches No mismatches allowed: cannot be used with --nogaps..
DETAILS:
* For help choosing scoring, see the README file.
* Gap (of length N) penalty is: (open+N*extend)
* To do alignment without affine gap penalty, set '--gapopen 0'.
* Scoring files should be matrices, with entries separated by a single
character or whitespace. See files in the 'scores' directory for examples.
turner.isaac@gmail.com (compiled: Oct 23 2013 19:08:54)
usage: ./bin/needleman_wunsch [OPTIONS] [seq1 seq2]
Needleman-Wunsch optimal global alignment (maximises score).
Takes a pair of sequences on the command line, or can read from a
file and from sequence piped in. Can read gzip files and FASTA.
OPTIONS:
--file <file> Sequence file reading with gzip support - read two
sequences at a time and align them
--files <f1> <f2> Read one sequence from each file to align at one time
--stdin Read from STDIN (same as '--file -')
--case_sensitive Use case sensitive character comparison [default: off]
--match <score> [default: 1]
--mismatch <score> [default: -2]
--gapopen <score> [default: -4]
--gapextend <score> [default: -1]
--scoring <PAM30|PAM70|BLOSUM80|BLOSUM62>
--substitution_matrix <file> see details for formatting
--substitution_pairs <file> see details for formatting
--wildcard <w> <s> Character <w> matches all characters with score <s>
--freestartgap No penalty for gap at start of alignment
--freeendgap No penalty for gap at end of alignment
--printscores Print optimal alignment scores
--zam A funky type of output
--printfasta Print fasta header lines
--pretty Print with a descriptor line
--colour Print with colour
EXPERIMENTAL (and buggy):
--nogapsin1 No gaps allowed in the first sequence
--nogapsin2 No gaps allowed in the second sequence
--nogaps No gaps allowed in either sequence
--nomismatches No mismatches allowed: cannot be used with --nogaps..
DETAILS:
* For help choosing scoring, see the README file.
* Gap (of length N) penalty is: (open+N*extend)
* To do alignment without affine gap penalty, set '--gapopen 0'.
* Scoring files should be matrices, with entries separated by a single
character or whitespace. See files in the 'scores' directory for examples.
turner.isaac@gmail.com (compiled: Oct 23 2013 19:08:54)
Baiscs:
$ ./needleman_wunsch CAGACGT CGATA
CAGACGT
C--GATA
Print alignment scores:
$ ./needleman_wunsch --printscores CAGACGT CGATA
CAGACGT
C--GATA
score: -15
Read from file (dna.fa):
>seqA
ACAATAGAC
>seqB
ACGAATAGAT
>seqC
ACGTGA
CAGAT
>seqD
GTGGACG
AGTA
$ ./needleman_wunsch --printscores --file dna.fa.gz
AC-AATAGAC
ACGAATAGAT
score: -3
ACGTGACAGAT
GTGGACGAGTA
score: -5
Reading from STDIN:
$ gzip -d -c dna.fa.gz | ./needleman_wunsch --stdin
AC-AATAGAC
ACGAATAGAT
ACGTGACAGAT
GTGGACGAGTA
is the same as:
$ gzip -d -c dna.fa.gz | ./needleman_wunsch --file -
Set different scoring systems:
$ ./needleman_wunsch --match 1 --mismatch 0 --gapopen -10 --gapextend 0 ACGTGCCCCACAGAT AGGTGGACGAGAT
Proteins:
| Query Length | Substitution Matrix | Gap Costs (open,extend) |
|---|---|---|
| <35 | PAM-30 | (9,1) |
| 35-50 | PAM-70 | (10,1) |
| 50-85 | BLOSUM-80 | (10,1) |
| 85 | BLOSUM-62 | (10,1) |
[Table from: http://www.ncbi.nlm.nih.gov/blast/html/sub_matrix.html]
gap (of length N) penalty: gap_open + N*gap_extend
NCBI BLAST Quote [from: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#Reward-penalty]:
Many nucleotide searches use a simple scoring system that consists of a "reward"
for a match and a "penalty" for a mismatch. The (absolute) reward/penalty ratio
should be increased as one looks at more divergent sequences. A ratio of 0.33
(1/-3) is appropriate for sequences that are about 99% conserved; a ratio of 0.5
(1/-2) is best for sequences that are 95% conserved; a ratio of about one (1/-1)
is best for sequences that are 75% conserved [1].
NCBI Gap (open, extend) values:
| open | extend |
|---|---|
| -5 | -2 |
| -2 | -2 |
| -1 | -2 |
| -0 | -2 |
| -3 | -1 |
| -2 | -1 |
| -1 | -1 |
Our default (for now) are:
gap_open/gap_extend: (-4,-1)
match/mismatch: (1,-2)
for help on choosing scoring matrices see: http://www.ebi.ac.uk/help/matrix.html
NCBI protein align matices from: ftp://ftp.ncbi.nih.gov/blast/matrices/
GPLv3
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
Feel free to contact me to request features. Bug reports are appreciated.
(turner.isaac@gmail.com)
- Add tests
- Finish adding the following options:
-
No unneeded gaps:
--nogapsin1
--nogapsin2
--nogaps -
Penalised gaps at ends:
--gapsonlyatendsin1
--gapsonlyatendsin2
--gapsonlyatends -
free gaps at ends:
--freestartgap
--freeendgap
Algorithms to investigate: Gotoh Hirschberg's algorithm using linear space Myer's bit-vector algorithm Combination of Myer's and Hirschberg's algorithm