File: fastBlockSearch.1.adoc

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# fastBlockSearch(1)

## NAME

fastBlockSearch - search loci matching protein block profiles

## SYNOPSIS

*fastBlockSearch* [options] seqs.fa fam.prfl

## DESCRIPTION  
  Searches hits (matches) of the blocks in the profile given by fam.prfl within the genomic sequences in the file seqs.fa.
  Hits are sorted increasingly by score, so the last displayed hit is the best one found in the region. The format is similar
  to that of the blockscore file (which is optionally generated by msa2prfl.pl): It shows coordinate, strand,
  mean odds-ratio score, and specificity of score, and the motif. 
  From the output users can chose regions with matching blocks to perform gene prediction with AUGUSTUS-PPX using the same block profile.

## EXAMPLE
  > fastBlockSearch --cutoff=1.1 chr4.103M.fa PF00225_seed.prfl
  
  Hits found in chr4 103000000 105000000
  Score:207.987
  Mult. score:4.83391
  1081586 unknown_M[5,13] -       2.32574 5.04633 .....YATRLKNI
  1103952 unknown_L       -       4.85363 6.75245 NAKTRIICTITP
  1103991 unknown_K       -       8.38065 9.92928 YRDSKLTRILQNSLG
  1104375 unknown_J       -       3.96065 6.79408 RSLFILGQVIKKL
  1106992 unknown_I       -       9.22487 7.64306 LVDLAGSE
  1115567 unknown_H[5,16] -       2.31869 5.58986 .....ESRHYGETKMN
  1116319 unknown_G       -       7.34282 8.29425 EIYNETITDLL
  1117092 unknown_F       -       5.10694 6.10274 VIPRAIHDIF
  1117146 unknown_E       -       9.43596 9.18891 QTASGKTYTM
  1117176 unknown_D[1,8]  -       5.73796 6.31532 .GTIFAYG
  1117399 unknown_B[1,7]  -       3.59083 5.03059 .CLDRVF
  1119420 unknown_A[0,8]  -       4.64107 6.44285 RVRPLNSR.

## OPTIONS

*--cutoff=c*::
  This minimum for the average log score of the motifs found can be used to adjust the sensitivity of the block search.
  The standard cutoff is 0.7, which is very sensitive but can give many false positive hits for smaller profiles.

## AUTHORS

Oliver Keller