Author: Azat Badretdinov (NCBI)


frameshift+ tool is intended 
*) to assist GenBank group to analyze bacterial genome submissions
*) to annotate better submitted WGS projects


Currently the tool is suited for performing the first task
The workflow has 4 stages:

*) extraction of sequences from input (.sqn) file
*) BLAST search vs bact_prot and CDD databases
*) analysis per se of the CDS's for frameshifts, partial hits and overlaps
*) BLAST search for marked sequences for user-friendly output

Algorithm of analysis:

*) frameshifts are flagged when two CDS's
  a1) are immediate neighbors in the contig or
  a2) all CDSs located between them do not have bact_prot hits and
  b)  have at least one pair of matching (GI) BLAST hits to bact_prot database
  Interestingly enough, it turned out that if mentioned conditions are met,
  the corresponding alignment regions of two CDS's to the common hit sequence
  are very consistent without significant gaps or insertions in the contig space
  between the CDSs
*) partial hits are flagged when a given CDS is persistently hitting only
  part of CDD profiles.
*) overlaps of parallel CDS's are flagged