Hi, any suggestion to retrieve multiple cDNA sequences from Ensembl site? I have to perform a multiple sequence alignment of different orthologs genes (cDNA only)
Ensemble biomart is a good way to get sequences for a select few genes. Have a look at this site http://www.ensembl.org/biomart/martview/c0b1f0703865a17bec39570cdec11c08 ... Click on Attributes select Sequences option -> then in the sequences panel select cDNA sequences -> finally click on results to get the sequences. Ensemble also has a ftp site incase you want to download all the cDNA sequences
Thank you very much.....but......How insert the genes I want to download in Biomart?
It seems I can download all cDNA sequences from all genes, but I need all hortologs of a specified gene (i.e coagulation F9)
Click on Attributes -> then click on Gene-> enter the ID's you want to retrieve or upload in a text file (a .txt file with one id per line)->select the appropriate source of your identifier eg. if you have entered a entrez gene id in the box then select entrez gene id in the dropdown menu ->Select sequences in the sequences panel -> click on results
I understand orthologs in your case as isoforms ... I hope thats correct ... or if you are interested in multispecie comparison for that gene than check the Multispecie comparision option
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