Mercurial > repos > bjoern-gruening > trna_prediction
view tRNAscan.xml @ 2:0fef99b5f63f draft default tip
apply patch from Nicola Soranzo
author | bjoern-gruening |
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date | Sun, 24 Mar 2013 14:35:48 -0400 |
parents | 65d282ef088e |
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<tool id="trnascan" name="tRNAscan" version="0.2.2"> <description>tRNA Scan</description> <requirements> <requirement type="package" version="1.3.1">tRNAscan-SE</requirement> <requirement type="python-module">biopython</requirement> </requirements> <command interpreter="python"> tRNAscan.py $organism $mode $showPrimSecondOpt $disablePseudo $showCodons -o $tabular_output $inputfile $fasta_output </command> <inputs> <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/> <param name="organism" type="select" label="Select Organism"> <option value="">Eukaryotic</option> <option value="-G">general tRNA model</option> <option value="-B">Bacterial</option> <option value="-A">Archaeal</option> <option value="-O">Mitochondrial/Chloroplast</option> </param> <param name="mode" type="select" label="Select Mode"> <option value="">Default</option> <option value="-C">Covariance model analysis only (slow)</option> <option value="-T">tRNAscan only</option> <option value="-E">EufindtRNA only</option> <option value="--infernal">Infernal cm analysis (max sensitivity, very slow)</option> <option value="--newscan">Infernal and new cm models</option> </param> <param name="disablePseudo" type="boolean" label="Disable pseudogene checking" truevalue="-D" falsevalue="" /> <param name="showPrimSecondOpt" type="boolean" label="Show primary and secondary structure components to Cove scores" truevalue="-H" falsevalue="" /> <param name="showCodons" type="boolean" label="Show codons instead of tRNA anticodons" truevalue="-N" falsevalue="" /> </inputs> <outputs> <data format="tabular" name="tabular_output" label="${tool.name} on ${on_string}: tabular" /> <data format="fasta" name="fasta_output" label="${tool.name} on ${on_string}: fasta" /> </outputs> <tests> <test> </test> </tests> <help> .. class:: warningmark **TIP** This tool requires *fasta* format. ----- **What it does** tRNAscan-SE was designed to make rapid, sensitive searches of genomic sequence feasible using the selectivity of the Cove analysis package. We have optimized search sensitivity with eukaryote cytoplasmic and eubacterial sequences, but it may be applied more broadly with a slight reduction in sensitivity . http://lowelab.ucsc.edu/tRNAscan-SE/ ----- **Organism** - search for eukaryotic cytoplasmic tRNAs: This is the default. - use general tRNA model: This option selects the general tRNA covariance model that was trained on tRNAs from all three phylogenetic domains (Archaea, Bacteria, and Eukarya). This mode can be used when analyzing a mixed collection of sequences from more than one phylogenetic domain, with only slight loss of sensitivity and selectivity. The original publication describing this program and tRNAscan-SE version 1.0 used this general tRNA model exclusively. If you wish to compare scores to those found in the paper or scans using v1.0, use this option. Use of this option is compatible with all other search mode options described in this section. - search for bacterial tRNAs This option selects the bacterial covariance model for tRNA analysis, and loosens the search parameters for EufindtRNA to improve detection of bacterial tRNAs. Use of this mode with bacterial sequences will also improve bounds prediction of the 3' end (the terminal CAA triplet). - search for archaeal tRNAs This option selects an archaeal-specific covariance model for tRNA analysis, as well as slightly loosening the EufindtRNA search cutoffs. - search for organellar (mitochondrial/chloroplast) tRNAs This parameter bypasses the fast first-pass scanners that are poor at detecting organellar tRNAs and runs Cove analysis only. Since true organellar tRNAs have been found to have Cove scores between 15 and 20 bits, the search cutoff is lowered from 20 to 15 bits. Also, pseudogene checking is disabled since it is only applicable to eukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode is used, searches will be very slow (see -C option below) relative to the default mode. ------ **Mode** - search using Cove analysis only (max sensitivity, slow) Directs tRNAscan-SE to analyze sequences using Cove analysis only. This option allows a slightly more sensitive search than the default tRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250 to 3,000 fold). Output format and other program defaults are otherwise identical to the normal analysis. - search using Eukaryotic tRNA finder (EufindtRNA) only: This option runs EufindtRNA alone to search for tRNAs. Since Cove is not being used as a secondary filter to remove false positives, this run mode defaults to "Normal" parameters which more closely approximates the sensitivity and selectivity of the original algorithm describe by Pavesi and colleagues. - search using tRNAscan only (defaults to strict search parameters) Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This mode will cause tRNAscan to default to using "strict" parameters (similar to tRNAscan version 1.3 operation). This mode of operation is faster (about 3-5 times faster than default mode analysis), but will result in approximately 0.2 to 0.6 false positive tRNAs per Mbp, decreased sensitivity, and less reliable prediction of anticodons, tRNA isotype, and introns. ----- **disable pseudogene checking** Manually disable checking tRNAs for poor primary or secondary structure scores often indicative of eukaryotic pseudogenes. This will slightly speed the program and may be necessary for non-eukaryotic sequences that are flagged as possible pseudogenes but are known to be functional tRNAs. ----- **Show both primary and secondary structure score components to covariance model bit scores** This option displays the breakdown of the two components of the covariance model bit score. Since tRNA pseudogenes often have one very low component (good secondary structure but poor primary sequence similarity to the tRNA model, or vice versa), this information may be useful in deciding whether a low-scoring tRNA is likely to be a pseudogene. The heuristic pseudogene detection filter uses this information to flag possible pseudogenes -- use this option to see why a hit is marked as a possible pseudogene. The user may wish to examine score breakdowns from known tRNAs in the organism of interest to get a frame of reference. ----- **Show codons instead of tRNA anticodons** This option causes tRNAscan-SE to output a tRNA's corresponding codon in place of its anticodon. ----- **Example** * input:: -Genome Sequence CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT ..... - organism : Mixed (general tRNA model) - mode : Default - disable pseudogene checking : not checked - Show both primary and secondary structure score components to covariance model bit scores : not checked - Show codons instead of tRNA anticodons : not checked * output:: Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Hit Name tRNA # Begin End Type Codon Begin End Score Origin -------- ------ ---- ------ ---- ----- ----- ---- ------ ------ CELF22B7 1 12619 12738 Leu CAA 12657 12692 55.12 Bo CELF22B7 2 19480 19561 Ser AGA 0 0 66.90 Bo CELF22B7 3 26367 26439 Phe GAA 0 0 73.88 Bo CELF22B7 4 26992 26920 Phe GAA 0 0 73.88 Bo CELF22B7 5 23765 23694 Pro CGG 0 0 60.58 Bo ------- **References** Todd M. Lowe and Sean R. Eddy tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucl. Acids Res. (1997) 25(5): 0955-964 doi:10.1093/nar/25.5.0955 </help> </tool>