Scroll to navigation



homGeneMapping - create summary of gene homology


homGeneMapping [options] --gtfs=gffilenames.tbl --halfile=aln.hal


homGeneMapping takes a set of gene predictions of different genomes and a hal alignment of the genomes and prints a summary for each gene, e.g.

•how many of its exons/introns are in agreement with genes of other genomes

•how many of its exons/introns are supported by extrinsic evidence from any of the genomes

•a list of geneids of homologous genes


Mandatory parameters


input hal file


a text file containing the locations of the input gene files and optionally the hints files (both in GTF format). The file is formatted as follows:

name_of_genome_1  path/to/genefile/of/genome_1  path/to/hintsfile/of/genome_1
name_of_genome_2  path/to/genefile/of/genome_2  path/to/hintsfile/of/genome_2
name_of_genome_N  path/to/genefile/of/genome_N  path/to/hintsfile/of/genome_N

Additional options


N is the number of CPUs to use (default: 1)


do not map between duplications in hal graph (default: off)


print detailed output (default: off)


Directory that contains the executable halLiftover If not specified it must be in $PATH environment variable.


print a GTF attribute with a list of all genomes, that are not aligned to the corresponding gene feature, e.g. hgm_unmapped \"1,4,5\"; (default; off)


a temporary file directory that stores lifted over files (default 'tmp/' in current directory)


file directory that stores output gene files (default: current directory)


prints disjunct sets of homologous transcripts to FILE, e.g.

# 0     dana
# 1     dere
# 2     dgri
# 3     dmel
# 4     dmoj
# 5     dper
(0, jg4139.t1) (0, jg4140.t1) (1, jg7797.t1) (2, jg3247.t1) (4, jg6720.t1) (5, jg313.t1)
(1, jg14269.t1) (3, jg89.t1) (5, jg290.t1)
Two transcripts are in the same set, if all their exons/introns are homologs and their are
no additional exons/introns.
This option requires the Boost C++ Library


retrieve hints from an SQLite database. In order to set up a database and populate it with hints a separate tool 'load2sqlitedb' is provided. For more information, see the documentation in docs/ (DATABASE ACCESS / SQLite) in the Augustus package. If both a database and hint files in 'gtffilenames.tbl' are specified, hints are retrieved from both sources.


homGeneMapping --noDupes --halLiftover_exec_dir=~/tools/progressiveCactus/submodules/hal/bin --gtfs=gtffilenames.tbl --halfile=msca.hal homGeneMapping --gtfs=gtffilenames.tbl --halfile=aln.hal --outdir=outdir --cpus=4


AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.


An exhaustive documentation can be found in the file /usr/share/doc/augustus/