常用的基因组注释工具

以下表格来自于:

A beginner’s guide to eukaryotic genome annotation

Mark Yandell & Daniel Ence. Nature Reviews Genetics 13, 329-342 (May 2012). doi:10.1038/nrg3174

三种基本的基因组注释方案

genome-annotation

常用注释工具

Software|Description|Refs —|—|+++ Ab initioand evidence-drivable gene predictors|| Augustus|Accepts expressed sequence tag (EST)-based and protein-based evidence hints. Highly accurate|66,67 mGene|Support vector machine (SVM)-based discriminative gene predictor. Directly predicts 5′ and 3′ untranslated regions (UTRs) and poly(A) sites|133 SNAP|Accepts EST and protein-based evidence hints. Easily trained|62 FGENESH|Training files are constructed by SoftBerry and supplied to users|72 Geneid|First published in 1992 and revised in 2000. Accepts external hints from EST and protein-based evidence|134 Genemark|A self-training gene finder|69,70 Twinscan|Extension of the popular Genscan algorithm that can use homology between two genomes to guide gene prediction|71 GAZE|Highly configurable gene predictor|74 GenomeScan|Extension of the popular Genscan algorithm that can use BLASTX searches to guide gene prediction|135 Conrad|Discriminative gene predictor that uses conditional random fields (CRFs)|136 Contrast|Discriminative gene predictor that uses both SVMs and CRFs|137 CRAIG|Discriminative gene predictor that uses CRFs|138 Gnomon|Hidden Markov model (HMM) tool based on Genscan that uses EST and protein alignments to guide gene prediction|73 GeneSeqer|A tool for identifying potential exon–intron structure in precursor mRNAs (pre-mRNAs) by splice site prediction and spliced alignment|139 EST, protein and RNA-seq aligners and assemblers| | BLAST|Suite of rapid database search tools that uses Karlin–Altschul statistics|31,32,33 BLAT|Faster than BLAST but has fewer features|42 Splign|Splice-aware tool designed to align cDNA to genomic sequence|44 Spidey|mRNA-to-DNA alignment tool that is designed to account for possible paralogous alignments|45 Prosplign|Global alignment tool that uses BLAST hits to align in a splice-site- and paralogy-aware manner|140 sim4|Splice-aware cDNA-to-DNA alignment tool|46 Exonerate|Splice-site-aware alignment algorithm that can align both protein and EST sequences to a genome|43 Cufflinks|Extension to TopHat. Uses TopHat outputs to create transcript models|54 Trinity|High-quality de novo transcriptome assembler|50 MapSplice|Spliced aligner that does not use a model of canonical splice junction|141 TopHat|Transcriptome aligner that aligns RNA sequencing (RNA-seq) reads to a reference genome using Bowtie to identify splice sites|51 GSNAP|A fast short-read assembler|52 Choosers and combiners| | JIGSAW|Combines evidence from alignment and ab initio gene prediction tools to produce a consensus gene model|78 EVidenceModeler|Produces a consensus gene model by combining evidence from protein and transcript alignments together with ab initio predictions using weights for both abundance and the sources of the evidence|79 GLEAN|Tool for creating consensus gene lists by integrating gene evidence through latent class analysis|80 Evigan|Probabilistic evidence combiner that use a Bayeisan network to weigh and integrate evidence from ab initio predictors, alignments and expression data to produce a consensus gene model|81 Genome annotation pipelines| | PASA|Annotation pipeline that aligns EST and protein sequences to the genome and produces evidence-driven consensus gene models|56,82 MAKER|Annotation pipeline that uses BLAST and exonerate to align protein and EST sequences. Also accepts features from RNA-seq alignment tools (such as TopHat). Massively parallel|10,83 NCBI|The genome annotation pipeline from the US National Center for Biotechnology Information (NCBI). Uses BLAST alignments together with predictions from Gnomon and GenomeScan to produce gene models|142 Ensembl|Ensembl’s genome annotation pipeline. Uses species-specific and cross-species alignments to build gene models. Also annotates non-coding RNAs|107 Genome browsers for curation| | Artemis|Java-based genome browser for feature viewing and annotation. Can use binary alignment map (BAM) files as input|99 Apollo|Java-based genome browser that allows the user to create and edit gene models and write their edits to a remote database|97 JBROWSE|JavaScript- and HTML-based genome browser that can be embedded into wikis for community work. Excellent for Web-based use|87 IGV|Genome browser that supports BAM files and expression data|143

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Z. Lu
Computer biologist, amature photographer, vintage fan and web lover.
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