Question: Genome annotation using EST assembly
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gravatar for psiwach29
2.8 years ago by
psiwach2910
psiwach2910 wrote:

i started working on est assembly and annotation of a plant species some months back, till that time complete genome sequence was not available. Now the species has its genome sequence sequenced and annotated and is in list of refgenomes. By the time i also finished EST pre-processing and assembly. Now can i still use my EST assembly data for gene finding (in the species genome sequence itself) so as to find some additional information as the genome has been annotated using homology based searches and ab initio methods? will it be relevant? can i go for mapping of est contigs and singletons on the genome, if yes what are tools available for this.

annotation est genome gene • 916 views
ADD COMMENTlink modified 2.7 years ago by Daniel Standage3.9k • written 2.8 years ago by psiwach2910
1

How large is the genome of your plant species? If not too large, you may be able to give Maker a go. Alternatively if the species is of interest to Ensembl Plants, they may be able to provide the annotation of that genome. Check it out with their helpdesk.

ADD REPLYlink written 2.8 years ago by Denise - Open Targets5.0k

genome size is nearly 15 Gb. The annotation report is available at NCBI and they have used EST data also for this. My question is how to use the EST assembly for finding something new and relevant in this case.

ADD REPLYlink written 2.8 years ago by psiwach2910

My guess, but ESTs don't sample enough unlike RNA-Seq particularly for a not so well studied organism unless many sources of ESTs exist under a variety of conditions. As the annotation is done using ESTs finding new transcribed regions should be rare. But you can try mapping the ests to the genome using any spliceaware mapper or a commandline blat and then use bedtools/samtools to get non-annotated regions which have coverage.

ADD REPLYlink written 2.8 years ago by microfuge1.1k

Ya, that sounds reasonable and relevant. Thanks a lot.

ADD REPLYlink written 2.8 years ago by psiwach2910

Blat would be a good starting option. It can do spliced alignments.

ADD REPLYlink written 2.8 years ago by microfuge1.1k
0
gravatar for Daniel Standage
2.7 years ago by
Daniel Standage3.9k
Davis, California, USA
Daniel Standage3.9k wrote:

PASA was one of the first, if not the first, EST assembly programs that existed long before RNA-Seq was in vogue. You splice-align transcripts using a program like GeneSeqer, and then PASA assembles the alignments. I haven't personally used it for annotation, but in its documentation PASA brandsĀ itself as an annotation tool.

ADD COMMENTlink written 2.7 years ago by Daniel Standage3.9k
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