Global pairwise sequence alignment derived from the needle program in the EMBOSS package Gapopens can be supplied under the sequence and enclosed in { }. In addition, it allows pairwise alignment of a large number of sequences. The software is developed in C/C++.
Nanjiang Shu
Senior researcher at SciLifeLab Stockholm
my_needle [options] seqfile1 seqfile2
OPTIONS:
<pre>
-list FILE Supply the pair list, one line a pair
-mode INT Pair mode, (default: 0)
0: pairs are two filenames of sequences
1: pairs are two seqIDs of sequences
2: do all-to-all pairwise alignment given a fasta file
with multiple sequences
-seqdb STR Indexed sequence database, this must be supplied when mode = 1
-m INT Output alignment format, (default: 0)
0: full pairwise alignment in EMBOSS needle format
1: full pairwise alignment in Fasta format
-table FILE Output tab delimited alignment info table to FILE
-type INT Set the alignment type. (default: 1)
0: for dna,
1: for aaseq
2: for shape strings
-matrix FILE Supply substitution matrix file. default is
NUC.4.4: for DNA alignment
BLOSUM62: for amino acid alignment
ShagMatrix6: for shape string alignment
-title1 STR Force the title of the first seqfile
-title2 STR Force the title of the second seqfile
-G FLOAT Penalty to open a gap, (default: 10.0)
-E FLOAT Penalty to extend a gap, default: 0.5)
-o FILE Output the alignment to outfile, (default: stdout)
-eg FLOAT Set endgapopen, (default: 10.0)
-ee FLOAT Set endgapextend, (default: 0.5)
-debug FILE Print the debug information to FILE
-endweight Enable endweight, default= No
-nogoarray Do not use the gapopen array even supplied
-threshold-seqdb-size INT
Threshold of seqdb file size in MB. (default: 1024)
If seqdb filesize < threshold, the whole file will be read
in to memory.
-max-align-size INT
Maximum align size in MB. (default: 1024)
max_align_size = seqlength1 * seqlengh2
-selpair INT Pair selection method for mode 2, (default: 1)
0: sequentially
1: randomly
-wordsize INT Wordsize for Kmer comparison, (default: 3)
-pkmer|-printkmerscore yes|no
Whether print KMer score, (default: no)
-h | --help Print this help message and exit
</pre>
Note that the sequence file should be in FASTA format.
Align the first sequence in oneseq.fa to all sequences in the 10seq.fa
$ ../my_needle oneseq.fa 10seq.fa
Align a large number of pairs of sequences by supplying sequence database and pairs of seqids
$ ../my_needle -list PF00008.pairlist -mode 1 -seqdb PF00008.fa -m 1 -o outfile.txt
All to all pairwise alignment given a file with multiple sequences
$ ../my_needle t2.fa -mode 2 -m 1 -table table1.txt
First get the software by
$ git clone https://github.com/nanjiangshu/my_needle
Then change to the directory "my_needle" by
$ cd my_needle
Then compile the software by running (note that you need gcc in order to compile the software)
$ make
For making the debug version, type
$ make debug
Gap penalties can be set under the sequence and enclosed in {}. A tag
*gpo: gap open
*gpe: gap extension
*tgpe: terminal gap extension
can be set directly after the left bracket {. If no tag is set, the default is the gap open array. A leading '#' will comment out the gap penalty array.
An example of input file with supplied gap open penalties:
>seq1
ASNLSKLFLSDSDA
{gpo: 10 -1000 10 10 10 10 10 10 10 10 10 10 10 10 }
{#gpe: 20 -1000 -10000 23 24 25 26 27 28 29 20 22 22 23 }
{#tgpe: 40 44 44 43 44 45 46 47 48 49 40 44 44 43 }
Email: [email protected]
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