Module: patis Description: Prediction of Alternative Translation Initiation Sites Version: 0.3 Last Edit: 30/01/14

Copyright © 2011 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_ensembl rje_seq rje_sequence rje_zen gablam

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module is designed to take as input files of 5' UTR and CDS sequences downloaded from EnsEMBL BioMart. Sequence headers should be named: EnsTranscript|EnsGene|GeneSymbol|Description

Commandline

General

basefile=X : Leader for *.utr5.fas and *.cds.fas sequences - should start with species [Homo_sapiens.GRCh37.p13]
orthspec=X : Species in which to look for conservation etc. of orthologues [Mouse]
orthbase=X : Basefile for AIC prediction on orthologous species [Mus_musculus.NCBIM37.64]
patisfas=T/F : Whether to output PATIS fasta file with extensions and AIC marked [True]
nonaug=LIST : Non-AUG codons to include in analysis (T or U) [CTG,GTG,ACG]
eorf=T/F : Whether to consider eORFs [True]
torf=T/F : Whether to consider tORFs [True]
ratings=X : Which rating scheme to use for AIC (biol2013/jan14) ['jan14']

BIOL3050

clonemap=T/F : Whether to map clones onto sequence file and check RE sites etc. [False]
minorf=X : Min length of extended ORF [20]
recut=LIST : List of recognition sequences for restriction enzymes ['CTCGAG','GCTAGC']
minfrag=X : Minimum length of fragment to clone [303]
mgcfile=FILE : Name of the MGC clone sequence file [mgc_clones.human.fasta]

GABLAM Options for Clone Mapping

gablamcut=X : Percentage identity cut-off for mapping to clones [95.0]
forks=X : Number of forks for GABLAM run [0]
blaste=X : E-value cut-off for BLAST search [1e-10]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Updated for 2011 BIOL3050 project and beyond.
    # 0.2 - Added option to determine non-AUG codons, primarily for BIOL2013 priming.
    # 0.3 - Added ratings=X       : Which rating scheme to use for AIC (biol2013/jan14) ['jan14']