Question: Annotating the transcripts of a de novo plant transcriptome
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gravatar for Biogeek
4.4 years ago by
Biogeek400
Biogeek400 wrote:

Hey,

 

 

Looking around for methodology on how to go about annotating a plant transcriptome. Whilst the information in papers tends to be simplified, and the internet does not really give a good simplied guide on how to go about this process, I've come here for a few simple answers.

1) What are the best databases available to annotate your Plant transcriptome with (de novo) assuming you are doing blastx on a stand a lone server and customized blastdb.

2) In regards to setting up your blastdb for blast x, what steps are involved. How do I for say, merge or parse several databases into 1 large custom database, so that the blastx can be performed once.

3) More broad question here; Once you get your annotation for the transcripts, how can you go about doing Pfam, Interpro?

Thanks.

 

 

 

 

ADD COMMENTlink modified 4.4 years ago by JC10k • written 4.4 years ago by Biogeek400
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gravatar for JC
4.4 years ago by
JC10k
Mexico
JC10k wrote:

1) Arabidopsis or Rice are the best studied plant models, you can start from there or using NCBI NR or RefSeq.

2) Get all your databases in fasta format, combine them into one large file (don't mix nucleotides/peptides) and format for Blast+. for example:

$ cat genes_1.fasta genes_2.fasta genes_3.fasta > all_genes.fasta

$ makeblastdb -in all_genes.fasta -out all_genes -dbtype nucl

3) Check HMMER+PFAM http://hmmer.janelia.org/download.html

Also check https://trinotate.github.io/

ADD COMMENTlink written 4.4 years ago by JC10k
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