genewise - options: output

All output options can be used at the same time. They are separated by the value to -divide option

-pretty

show pretty ascii output, as see in Section 2

-pseudo

For genes with frameshifts, mark them as pseudo genes

-genes

show gene structure - as

Gene 1
  Gene 1386 3963
    Exon 1386 1493
    Exon 1789 1935
    Exon 2084 2294
    Exon 2388 2480
    Exon 2794 2868
    Exon 3073 3228
    Exon 3806 3963
//

-para

show parameters

-sum

show summary output. Shows output as

Bits   Query         start end Target      start end   idels introns
230.57 roa1_drome     26  347 HSHNRNPA     1386 3963    0    6

This is useful for parsing, but probably if you want to do something like that you want to get hold of the API directly.

-cdna

show cDNA Show a fasta format of the predicted cDNA sequence

-trans

show protein translation Show a fasta format of the predicted protein sequence. Breaks on frameshifts

-pep

show predicted peptide. Shows predicted peptide, including frameshifts, which are X's in the proteins

-ace

ace file gene structure - ACeDB subsequence model

  Sequence HSHNRNPA
  subsequence HSHNRNPA.1 1386 3963
  
  Sequence HSHNRNPA.1
  CDS
  CDS_predicted_by genewise 0.00
  source_Exons 1 108
  source_Exons 404 550
  source_Exons 699 909
  source_Exons 1003 1095
  source_Exons 1409 1483
  source_Exons 1688 1843
  source_Exons 2421 257

-gff

Gene Feature Format file - useful for programs which also support GFF

  HSHNRNPA GeneWise cds_exon 1386 1494 0.00 + 0
  HSHNRNPA GeneWise cds_exon 1789 1936 0.00 + 0
  HSHNRNPA GeneWise cds_exon 2084 2295 0.00 + 0

-gener

raw gene structure - a debugging output

-alb

show logical AlnBlock alignment - a debugging output

-pal

show raw matrix alignment - a debugging output

-block

[50] Length of main block in pretty output

-divide

[//] divide string for multiple outputs