I have a palindromic sequence that I need to find in Brugia malayi genome. It is only 13 nucleotides. I tried using BLASTn but it failed the character requirement. I need to find it upstream of the ORF about maximum -4000 position. It should not be a part of the ORF. Can anybody suggest a tool to pull the genome database from wormbank and search my sequence in it? So far, I had trouble even pulling out the Brugia malayi data from the wormbank. It is linux coded. Can anybody suggest an alternate to linux?
Amruta, those files on wormbase are not Linux-specific. The sequence files are just gzipped FASTA files, and even Windows can unzip a gzip file if you just install an open source compression tool that handles gzip. FASTA files are just text files, once uncompressed. The annotation files are just gzipped GFF files (general feature format files) - again, just plain text once uncompressed.
So, just grab yourself a free or open source compression program like 7-zip or Zipgenius (if you are using a Windows computer) and download the files you need from www.wormbase.org and then you can do your custom search.
A Mac computer running OS X already has the ability to unzip gzip files.
Hello Michael, I tried opening the .ga file on my computer. It unzipped but I am unable to open it. It is a 100mb file. Can you suggest me a software to open fasta file?
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