Extending Protein domain predictors to detect discontinuous domains DomEx USAGE: Mandatory arguments: ./DomEx.pl -seqname sequence_name Optional arguments: -workdir workdir: the work directory.Defaut:'./workspace' -b b_value: the cutoff of the parameter b(0.1<=b<=0.9). Default: 0.1. Users can change these defaut values from line 23 to 31 of DomEx.pl
For example: ./DomEx.pl -seqname Targetname -b 0.3
Notice:
(1)the Tegetname.fasta and Targetname.sd should be put in the directory workdir/Targetname.Check the example in the workspace,please.
(2)Targetname.sd: The file of predicted domain segments predicted by any domain predictor. The format is like :targetname\tsequencelenth\tsegmentnum\tsegments\n. If users want to combine DomEx with ThreaDOm, install ThreaDom, and copy the segment prediction result to target.sd.
(3)The program is designed on the PBS-based cluster. Users have to modify the programs if running on workstation.
For test: There is an example in ./output/S50. User can add a task to crontab for multi-call dDomEx.pl, or excute "./DomEx.pl -seqname S50" several times mannully. User can also check the check.txt file for the running state.
For users who want to predict domain boundaries by ThreaDom: (1)Download ThreaDom package from http://zhanglab.ccmb.med.umich.edu/ThreaDom/ , or subimit your sequence online. (2)copy prediction result to Targetname.sd( for example T50.sd) (2)excute ./DomEx.pl -seqname Targetname
About Domain nonreduntant library: This library file is too large to upload to github. Users can extract the single domain library from CATH,SCOP,Pfam, or downlaod from http://isyslab.info/DomEx.
zhidong xue zdxue@hust.edu.cn