First Question

[njt638]

Hello, I am a new graduate student and I am hoping to be able to do some sequence analysis, but here is the problem: I have never done anything like this before and I don't know anyone with the experience. So I am hoping this forum can help me.

I want to investigate some genomic data that is present in an sra file. I am specifically looking for sequences similar to a gene with a known full cDNA sequence. How can I do this? what software do I need? Is it even possible?

If anyone can help that would be great

Also, nice to meet you

[samanta]

Everything is possible. The question is what skills you have to make it possible. Can you write small perl codes? Can you download and install readily available programs?

Many aspects of your question are not clear from the short description. Are you trying to find SNPs? Are you trying to find genes in a related organism? So, let me create one example and answer it. Let us say you have a SRA file with Illumina gene (RNAseq) data from one organism (one type of mosquito - A) and you have full length cDNA from a related organism (different type of mosquito - B). You want to figure out the homologous gene in mosquito A.

In that case, you can use Bowtie to align all RNAseq reads to the cDNA, and then assemble the matching reads with any simple program like cap3.

You can see that I made many assumptions in the above description. Any change in the assumption (let's say 454 data instead of Illumina) will change the answer. So you have to be more specific.

You may read some of the descriptions in these commentaries (http://www.homolog.us/blogs/category/introductory-2/) to learn about wide variety of analysis tools and skills that all fall under bioinformatics. It is not all about finding programs, downloading and running.