Predicting Full Length Cdna Sequences From A Fasta Sequence File

Question

[Prakki Rama]

Hi,

Can i consider an sequence to be full-length cDNA, if the ORF in the sequence aligns with ~99%-100% identity, with 100% coverage to the reference protein? The species i work on does not have any nearest reference.

Could i please know, if there are any tools/scripts available which can run locally to predict full-length cDNA sequences. I know tools like TargetIdentifier and Full-lengther which can run online, but they eat a lot of time (for running BlastX). (edit: bit confused with target identifier terminology (eg: sense complete and partial), full-lengther does not work any more)

I would also like to appreciate if someone guides me in this issue. Pleae spare if i am not able to put properly.

Thanks in advance.

[Pappu]

As far I understood, you want to find out genes in your fasta file? Then glimmer is a good option.

[Prakki Rama]

@pappu: Thank you, but is not glimmer is especially designed for microbial sequences? I used augustus to do that in that place which gives out the most possible ORF's.

[Pappu]

Did you check out the papers by Gunnar Rätsch on ORF predictions?

[Prakki Rama]

you mean mGene? My species does not have Genome either to train the model.

Answer 1

[Raghul]

Hi There is one easy way to get full length predicted sequences with OrfPredictor. But Orf-predictor need blastx result. So find a very closely & well annotated/completely sequenced genomes for your dataset.Collect all the protein sequences & create a database using standalone BLAST (makeblastdb command ). Do blastx with this newly created protein database.Standalone blast will finish in few seconds. Remember to give the parameters -num_alignments 1 & -num_descriptions 1. Uploading the result in Ful-lengther will fetch the result in 30 minutes or so.

This method works when you have complete sequences, if u have partial sequences u get partial CDS (naturally!) I got the results this way & it is fine, also output is both protein & CDS!http://proteomics.ysu.edu/tools/OrfPredictor.html

good luck raghul

[Prakki Rama]

Thank you raghul. I tried a similar apporach using BLAT. It helped me to get the results quickly.