I found a lot of web-based tools, but they can't be used for large files.
There are several scripts that you can use such as bp_sreformat.pl in BioPerl (http://www.bioperl.org/wiki/Main_Page) or BioPython (http://biopython.org/wiki/Seq).
If you want to use a graphical interface I think that other option may be Galaxy (https://usegalaxy.org/). It can handle big datasets. For your problem, there is an application in the EMBOSS tools section, with the name TransSeq that you can use with a loaded dataset.
There are several scripts that you can use such as bp_sreformat.pl in BioPerl (http://www.bioperl.org/wiki/Main_Page) or BioPython (http://biopython.org/wiki/Seq).
If you want to use a graphical interface I think that other option may be Galaxy (https://usegalaxy.org/). It can handle big datasets. For your problem, there is an application in the EMBOSS tools section, with the name TransSeq that you can use with a loaded dataset.
Thanks a lot Aureliano! That is exactly what I was looking for (https://usegalaxy.org).
Hi Christian, what do you mean by cDNA database? Are you developing it or did you download it. If you are creating it, which I do not undrestand, you should be more specific. Is it prokaryotic, eukaryotic,.... Or even mixture? I can send you several scripts, but be more specific and explain why you want translated database and not nucleotide? The choise depend if you want to blast close species with blastn or more distinct species with blastx. Moreover, if you want to have miRNA database you need specific script which can calculate secondary strucuture before search. And for miRNA I really do not understan why you need peptide sequence since miRNA does not code any peptide...how did you prepare library for miRNA? It will result in diferent proportion of mature and pre-miRNA. So my recommendation would be not translate.
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