finding new peptides from transcriptom?

Question

[alirezaei3333]

i want to explain whole my work. i have transcriptome of scorpion. we need to find the peptides with 12 length and cystein rich. i dont familiar with any bioinformatic program. anyway, would you please to obtain this peptide, which step should be done?

Answer 1

[GenoMax]

Based on your previous posts, it is not completely clear what data you have.

You have "transcriptome of a scorpion" but

• you never said how it was generated.
• you were looking to find putative genes at one point (how find the putative gen from cdna library? ) but it is not clear if you have done that.
• you were then looking for cysteine rich peptides (the best and user-friendly tools for blast peptides ) but decided that you could not use online blast.

To address the original question: If you know the pattern that you are looking for then you can use a program like fuzzpro from EMBOSS, (link provided for reference you will need to install EMBOSS locally if you have a large amount of data to process). There are several other programs in EMBOSS package that can be used for motif searches.

If you truly have no bioinformatics experience and can't use the command line then you are going to need help of type that would be hard to provide via an online forum. You should try to collaborate with a local bioinformatician who can assist you with this analysis.

[alirezaei3333]

i obtain via Illumina Next Generation Sequencing then i isolatated favor sequnces with python and now i am looking for a blast tools