LOHIRIA is a easy-to-use tool for identification of regions in longer alignment which fulfil two thresholds: minimal length of an region and minimal identity. Because we are dealing only with identity, this tool can be used both for nucleotide and protein alignments. As a input LOHIRIA can use output from many standard, pairwise alignment programs, especially FASTA and BLAST. Program can identify multiple windows in one alignment and can deal with overlapping windows as well. Results can be presented in text form, tables or dynamic web pages.
Usage: lohira [OPTION]... FILE...
Localization Of High Identity Regions In Alignments
Mandatory arguments to long options are mandatory for short options too.
-l, --length=LENGTH minimum window length (default is 200)
-t, --threshold=THRESHOLD minimum identity threshold (default is 0.8)
-d, --details show overlapping windows
-a, --limit mamimum number of alignments (default is 50)
The value 0 means unlimited.
-i, --input=FORMAT input format, posible values:
auto (default)
blast:xml
blast:tab
fasta
-o, --output=FORMAT output format, posible values:
text (default)
text:brief
text:details
html
-w, --write=FILE write result into the file
-h, --help print this help message
Input format notes:
* xml blast(n|p) output has to be run with parameter -outfmt 5
* tabular blast(n|p) output with parameter
-outfmt "7 qseqid sseqid qstart qend sstart send stitle qseq sseq"
* fasta with output format -m 10
| jan dot paces at img dot cas dot cz | timestamp: 2016-12-08 14:29:22 |