I have to find a 13 nucleotide sequence in a genome. I have the fasta file of the genome. But, I don't have the software that can open the file. Can anyone suggest to me software to open and analyze the particular 13 nucleotide pattern/ sequence in my fasta file?
You can open fasta files in most of the text editors on different computing platforms. Softwares like notepad, or .txt file handlers or Word can be used.
I am not sure about the 13 nucleotide sequence in the genome. I hope you must have a reference sequence which you will be comparing with to know the difference between the two sequences.
There are so many websites which can handle large fasta files direct.
Some other bench softwares which are in use include CLCviewer, Bioedit and many more. I hope that was bit helpful.
In MS Word. Pull down Menu, File -> Open -> enable "All Files" in the pull down menu so you can see your file. Then choose the "text encoding" probably choose (western AsciII). check the preview window of the dialogue box to check how the file looks to MS Word. Save this file as a text only file (.txt). Then paste your 13 nucleotide sequence into the "Find" window. from the "Edit Menu". So pulldown Menu "Edit"Choose "Find" paste your sequence into this window and hit return, MS word should be able to find the 13 nucleotide sequence. You may have to use the find replace capability to replace any hidden characters (carriage returns, etcetera) which may or not be imbedded in your file.
Unless you are ONLY interested in perfect matches, and all the 13 nucleotide positions specify a particular base, a text-based tool will not give you a satisfactory answer. There are some excellent online tools for this type of analysis. Check out the tools at MEME, http://meme.nbcr.net/meme/
I would suggest you not to use MS word to open large genome fasta file as it used to hang many times. Beter use notepad or any text editor (eg. geditor in linux etc.) for the same and ctrl+F ur 13 nucleotide seq. Dnt forget to enable wordwrap after deleting new line character at the end of each line in ur seq otherwise u might not find ur seq of interest.
Enjoy.
By the way, MEME is very good option or u can also try BLASTn by enabling the option to align two or more sequences (I think it should work).
I tried Blast, but it has a minimum number of nucleotide requirement. 13 is too less for it to align. Also, the sequence I am searching cannot be a part of a ORF. It has to be upstream of ORF. Can MEME help me with that?
Yes, MEME will work. Not the same length cutoff as BLAST, and you can filter out ORFs post-hoc, or instruct MEME to scan pre-selected sequences (wherein you have excluded ORFs).
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