tRNA prediction (tRNAscan)（tRNAscan-SE程序进行tRNA预测）

功能简介

分析模块，默认输入Fasta格式的细菌完成图和草图组装结果。采用tRNAscan-SE程序进行tRNA预测，封装了Software：tRNAscan-SE-1.3.1

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.

分析模块引用了 tRNAscan-SE-1.3.1 软件（http://lowelab.ucsc.edu/tRNAscan-SE/）。

相关文献如下所示：

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

相关参数说明：

Organism

  • search for eukaryotic cytoplasmic tRNAs:

  • use general tRNA model:

    This option selects the general tRNA covariance model that was trainedon tRNAs from all three phylogenetic domains (Archaea, Bacteria, andEukarya). This mode can be used when analyzing a mixed collection ofsequences from more than one phylogenetic domain, with only slightloss of sensitivity and selectivity. The original publicationdescribing this program and tRNAscan-SE version 1.0 used this generaltRNA model exclusively. If you wish to compare scores to those foundin the paper or scans using v1.0, use this option. Use of this optionis compatible with all other search mode options described in thissection.

  • search for bacterial tRNAs

    This option selects the bacterial covariance model for tRNA analysis,and loosens the search parameters for EufindtRNA to improve detectionof bacterial tRNAs. Use of this mode with bacterial sequenceswill also improve bounds prediction of the 3' end (the terminal CAAtriplet).

  • search for archaeal tRNAs

    This option selects an archaeal-specific covariance model for tRNAanalysis, as well as slightly loosening the EufindtRNA searchcutoffs.

  • search for organellar (mitochondrial/chloroplast) tRNAs

    This parameter bypasses the fast first-pass scanners that are poor atdetecting organellar tRNAs and runs Cove analysis only. Since trueorganellar tRNAs have been found to have Cove scores between 15 and 20bits, the search cutoff is lowered from 20 to 15 bits. Also,pseudogene checking is disabled since it is only applicable toeukaryotic cytoplasmic tRNA pseudogenes. Since Cove-only mode isused, searches will be very slow (see -C option below) relative to thedefault 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 defaulttRNAscan + EufindtRNA -> Cove mode, but is much slower (by approx. 250to 3,000 fold). Output format and other program defaults areotherwise identical to the normal analysis.

  • search using Eukaryotic tRNA finder (EufindtRNA) only:

    This option runs EufindtRNA alone to search for tRNAs. Since Cove isnot being used as a secondary filter to remove false positives, thisrun mode defaults to "Normal" parameters which more closelyapproximates the sensitivity and selectivity of the original algorithmdescribe by Pavesi and colleagues.

  • search using tRNAscan only (defaults to strict search parameters)

    Directs tRNAscan-SE to use only tRNAscan to analyze sequences. Thismode will cause tRNAscan to default to using "strict" parameters(similar to tRNAscan version 1.3 operation). This mode of operationis faster (about 3-5 times faster than default mode analysis), butwill 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.

  • search using Infernal cm analysis only (max sensitivity, very slow)

  • search using Infernal and new cm models instead of Cove

disable pseudogene checking

Manually disable checking tRNAs for poor primary or secondarystructure scores often indicative of eukaryotic pseudogenes. Thiswill slightly speed the program and may be necessary for non-eukaryoticsequences that are flagged as possible pseudogenes but are known to befunctional tRNAs.

Show both primary and secondary structure score components to covariance model bit scores

This option displays the breakdown of the two components of thecovariance model bit score. Since tRNA pseudogenes often have onevery low component (good secondary structure but poor primary sequencesimilarity to the tRNA model, or vice versa), this information may beuseful in deciding whether a low-scoring tRNA is likely to be apseudogene. The heuristic pseudogene detection filter uses thisinformation to flag possible pseudogenes -- use this option to see whya hit is marked as a possible pseudogene. The user may wish toexamine score breakdowns from known tRNAs in the organism of interestto get a frame of reference.

Show codons instead of tRNA anticodons

This option causes tRNAscan-SE to output a tRNA's corresponding codonin place of its anticodon.