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CpGAT - A Comprehensive Pipeline for Genome Annotation  

2014-04-06 23:50:19|  分类: 生物信息编程 |  标签: |举报 |字号 订阅

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CpGAT - A Comprehensive Pipeline for Genome Annotation - xiaofeng1982 - Tiger-Leon
 


CpGAT is a comprehensive tool for annotating genomic regions up to 500 kilobases. CpGAT uses EVM (EVidence Modeler) to evaluate GenomeThreader protein/transcript spliced alignments together with ab initio gene finder results (BGFGeneMark, and Augustus). In addition, some PASA functions are used to aggregate splice variant models. Output file formats include GFF3Gbrowse text, and FASTA (transcript, CDS and translation). The gene models are also displayed in PlantGDB's genome browser and yrGATE annotation tool. Click to view CpGAT Schema (Liu et al., 2010, Manuscript in Preparation)

Note: CpGAT is also available at our BIoExtract website. BioExtract publishes an external link to access the CpGAT tool (login account required)

More Information on CpGAT...

Selecting input sequence: Genome sequence is automatically uploaded from genome browsers; alternatively, paste or upload genomic sequence (up to 500 kb). Next, select or upload any combination of protein/transcript datasets for spliced-alignment. Finally, select splice models and any additional options, and click Submit. Sequences must be provided in FASTA format.

Output: CpGAT may take 2-5 minutes or more to process data, depending on the genome region size and number and size of datasets chosen. When complete, a CpGAT output window will display links to output files in various formats: GFF3, Gbrowse upload, and FASTA. Refresh your genome browser window to view new annotation tracks (listed under User_Auto_Annotation). To remove CpGAT tracks, click Delete Annotation from the output window, and refresh your genome browser again.

Reference/Masking Data Sources: User-specified protein/transcript datasets are pre-filtered against the genome region using blastn and blastx prior to spliced aligment. The GenomeThreader splice-aligned exon ORFs are evaluated for similarity to vs. UniRef 90 Viridiplantae using blastx prior to EVM. Genome sequence is n-masked for GenomeThreader analysis and ab inito gene finding usingTIGR4.0 and MIPS-REdat masking libraries.

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