TransposonPSI involves a PSI-blast search of a protein or nucleotide sequence against a set of profiles of proteins corresponding to major clades/families of transposon Open Reading Frames.
Note: This repo is created just for ease of creating a conda package for TransposonPSI, please refer to the original site at http://transposonpsi.sourceforge.net/ if you have any questions.
This is most useful to:
-identify proteins with similarities to known families of transposon ORFs.
-identify (degenerate) regions in genome sequences with homology to known transposon ORFs.
Run like so:
% ./transposonPSI.pl
usage: ./transposonPSI.pl $fastaFile prot|nuc
Two output files are created:
fastaFile.topHits(forprotsearches)andfastaFile.allHits (for nuc searches)
The hits are reported in btab format. See the script ‘scripts/BPbtab’ for information on the tab-delimited output format.
The .topHits file contains only the single best hit (by blast score).
The .allHits file contains each match scoring above the 1e-5 E-value default.
On ‘nuc’ searches, gff3 files are automatically generated for all hits and only the best hits per genomic locus.
Installation Requirements:
-you must have NCBI blast installed, including blastall and blastpgp
-bioPerl
Transposon families included by the profiles are:
cacta.chkp gypsy.chkp ISa.chkp isc1316.chkp ltr_Roo.chkp mariner.chkp P_element.chkp
DDE_1.chkp hAT.chkp ISb.chkp line.chkp mariner_ant1.chkp MuDR.chkp TY1_Copia.chkp
See the transposon_PSI_LIB/ directory for the reference sequences corresponding to the above families.
TransposonPSI
TransposonPSI involves a PSI-blast search of a protein or nucleotide sequence against a set of profiles of proteins corresponding to major clades/families of transposon Open Reading Frames.
Note: This repo is created just for ease of creating a conda package for TransposonPSI, please refer to the original site at http://transposonpsi.sourceforge.net/ if you have any questions.
This is most useful to: -identify proteins with similarities to known families of transposon ORFs. -identify (degenerate) regions in genome sequences with homology to known transposon ORFs.
Run like so:
% ./transposonPSI.pl
usage: ./transposonPSI.pl $fastaFile prot|nuc
Two output files are created: fastaFile.topHits(forprotsearches)andfastaFile.allHits (for nuc searches)
The hits are reported in btab format. See the script ‘scripts/BPbtab’ for information on the tab-delimited output format. The .topHits file contains only the single best hit (by blast score). The .allHits file contains each match scoring above the 1e-5 E-value default.
On ‘nuc’ searches, gff3 files are automatically generated for all hits and only the best hits per genomic locus.
Installation Requirements: -you must have NCBI blast installed, including blastall and blastpgp -bioPerl
Transposon families included by the profiles are: cacta.chkp gypsy.chkp ISa.chkp isc1316.chkp ltr_Roo.chkp mariner.chkp P_element.chkp DDE_1.chkp hAT.chkp ISb.chkp line.chkp mariner_ant1.chkp MuDR.chkp TY1_Copia.chkp
See the transposon_PSI_LIB/ directory for the reference sequences corresponding to the above families.
Questions, comments, etc?
contact: Brian Haas bhaas@broadinstitute.org