# extrinsic information configuration file for AUGUSTUS # # protein hints # include with --extrinsicCfgFile=filename # date: 16.10.2007 # Mario Stanke (mstanke@gwdg.de) # source of extrinsic information: # M manual anchor (required) # P protein database hit # E EST/cDNA database hit # C combined est/protein database hit # D Dialign # R retroposed genes # T transMapped refSeqs # W wiggle track coverage info from RNA-Seq [SOURCES] M RM E W # # individual_liability: Only unsatisfiable hints are disregarded. By default this flag is not set # and the whole hint group is disregarded when one hint in it is unsatisfiable. # 1group1gene: Try to predict a single gene that covers all hints of a given group. This is relevant for # hint groups with gaps, e.g. when two ESTs, say 5' and 3', from the same clone align nearby. # [SOURCE-PARAMETERS] # feature bonus malus gradelevelcolumns # r+/r- # # the gradelevel colums have the following format for each source # sourcecharacter numscoreclasses boundary ... boundary gradequot ... gradequot # [GENERAL] start 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 stop 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 tss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 tts 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 ass 1 1 0.1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 dss 1 1 0.1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 exonpart 1 .992 .985 M 1 1e+100 RM 1 1 E 1 1 W 1 1.02 exon 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 intronpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 intron 1 .34 M 1 1e+100 RM 1 1 E 1 1e4 W 1 1 CDSpart 1 1 .985 M 1 1e+100 RM 1 1 E 1 1 W 1 1 CDS 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 UTRpart 1 1 .985 M 1 1e+100 RM 1 1 E 1 1 W 1 1 UTR 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 irpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 nonexonpart 1 1 M 1 1e+100 RM 1 1.15 E 1 1 W 1 1 genicpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 [GROUP] # replace 'none' by the names of genomes with src=W and src=E hints in the database none [GENERAL] start 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 stop 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 tss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 tts 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 ass 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 dss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 exonpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 exon 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 intronpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 intron 1 .1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 CDSpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 CDS 1 .1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 UTRpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 UTR 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 irpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 nonexonpart 1 1 M 1 1e+100 RM 1 1.15 E 1 1 W 1 1 genicpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 [GROUP] # replace 'none' by the names of genomes with src=M hints in the database none [GENERAL] start 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 stop 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 tss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 tts 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 ass 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 dss 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 exonpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 exon 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 intronpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 intron 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 CDSpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 CDS 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 UTRpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 UTR 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 irpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 nonexonpart 1 1 M 1 1e+100 RM 1 1.15 E 1 1 W 1 1 genicpart 1 1 M 1 1e+100 RM 1 1 E 1 1 W 1 1 [GROUP] other # # Explanation: # # In comparative gene prediction, hints can be integrated for multiple species. # In order to have different extrinsic config settings for different species, # multiple [GENERAL] tables are specified. Each table is followed by a [GROUP] section, # a single line, in which a subset of the species is listed, for which the table is valid. # Use the same species identifiers as in the MSA and in the phylogenetic tree. # If a species is not assigned to any of the tables, all hints for that species are # ignored. To assign all species to a single table, the key 'all' can be used instead of itemizing # every single species identifier. Use the key 'other' to specify a table for all species, not # listed in any previous table. When the key 'none' is specified the table is skipped. # Note that the source RM must be specified in case that the softmasking option is turned on. # Also note that all tables have the same dimension, i.e. each table must contain all sources # listed in the section [SOURCES], even sources for which no hints exist for any of species # in group.