Institute of Molecular Genetics (main page)
Dept. Genomics and Bioinformatics

LOHIRIA: Localization Of High Identity Regions In Alignment


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)
  -o, --output=FORMAT          output format, posible values:
                               text (default)
  -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


Previous versions:


Lohiria can be used for detection of possible horizontal tranfer. Check pipeline example here


article in preparation
jan dot paces at img dot cas dot cz timestamp: 2016-12-08 14:29:22