uniprobe2meme

Usage:

uniprobe2meme [options]

Description

Converts UNIPROBE matricies from standard input into a MEME motif file suitable for use with MEME Suite programs. You may concatenate files for more than one motif.

Input

Reads UNIPROBE matricies from standard input.

Concatenated UNIPROBE files describe one or more motifs. Each motif has a header line and a position-weight matrix.

Example
Arid3a_primary A: 0.179645793597971 0.210100830864919 0.18297957170479 0.218158426414591 0.0870705802557497 0.0435293344848582 0.695645391274696 0.886231513936226 0.105526350481291 0.112302355076614 0.815030478488063 0.719906706101697 0.598597229834128 0.469818137392637 0.233954380973979 0.267838631058226 0.240559605564699 C: 0.266648735950844 0.218430924209102 0.213084153545938 0.203797703013696 0.110886816294852 0.0958703394836635 0.0104078225875119 0.00354104133931097 0.00470109424317215 0.181644431061179 0.045569847543415 0.0821358973477016 0.0458429114703258 0.282556547844063 0.229160661497462 0.231747372592299 0.300737862311012 G: 0.382823288901203 0.353259680323954 0.340965693699501 0.18760023292416 0.0821358973477016 0.045569847543415 0.181644431061179 0.00470109424317215 0.00354104133931097 0.0104078225875119 0.0958703394836635 0.110886816294852 0.0853202791343203 0.0573452956112842 0.190290024780233 0.133765504128307 0.201112183210201 T: 0.170882181549982 0.218208564602024 0.262970581049772 0.390443637647554 0.719906706101697 0.815030478488063 0.112302355076614 0.105526350481291 0.886231513936226 0.695645391274696 0.0435293344848582 0.0870705802557497 0.270239579561226 0.190280019152016 0.346594932748325 0.366648492221168 0.257590348914088 Arid5a_primary A: 0.177322769961677 0.160221841004699 0.852203018833067 0.961248539596473 0.0565398220443113 0.930330589214641 0.019950864688249 0.0411316382396864 0.233918811349109 0.339577406902739 0.285389335391289 0.572142692856743 0.285668980971376 0.342798848206545 C: 0.428313310855555 0.324571292259573 0.0267326703147277 0.00379831572782298 0.00400812936891674 0.0051379987521542 0.0141888286179256 0.0875059354874809 0.027935175632631 0.352987545623934 0.13471914100935 0.0784175907242025 0.184067740053308 0.230459946341397 G: 0.22903578216647 0.0324446387621822 0.073955464568744 0.0101183390736629 0.00787744708407332 0.00713820083753976 0.00678864795483705 0.0390246666857379 0.519604520580082 0.184315929397724 0.268289476918125 0.190434321213762 0.262198874546343 0.153946120466092 T: 0.165328137016298 0.482762227973546 0.0471088462834612 0.0248348056020407 0.931574601502699 0.057393211195665 0.959071658738988 0.832337759587095 0.218541492438178 0.123119118075603 0.311602046681237 0.159005395205293 0.268064404428973 0.272795084985967

Output

Options

Option Parameter Description Default Behaviour
General Options
-numseqs# seqs Assume that the motif was created from # seqs sites. Assume the motif was based on 20 sites.
-truncate_names Truncate motif names at the first underscore in the UNIPROBE ID. If the UNIPROBE ID was "Arid3a_primary" then it would be shortened to just "Arid3a". Keep the full UNIPROBE ID.
-sgsg_file_name File containing motif name and ID in 2 columns. The second column is substituted for MOTIF_NAME in the URL if -url is given. The motif name is substituted for MOTIF_NAME.