Use this forum for general bioinformatics questions, or questions regarding genomics, proteomics, etc.
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I have a bacterial genome sequence (inhouse-sequencing of serotype X) and gene sequences from already described serotypes A, B, C and so on. My task is to find out which genes from the serotypes A (...) are in my serotype X. For that I wanted to perform an alignment for any similarities between the sequences (In case of any mutations). My problem is that the sequence of my genome is too long for any internet tool I've found (All tools say that the maximum file size for my genome sequence is reached). It's size is about 2.5 MB. Are there any online tools which can handle this file size or is there a software for downloading?
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I don't know of any free online tools, maybe you can browse the seqanswers forum for that. If you have some programming knowledge, you could try R or Matlab. There are several not free porgrams that will do this. for instance geneious and bionumerics (disclaimer: I work for the company that develops bionumerics). For both, you can download free trial versions.
To speed up your analysis, I would advise you to concatenate the sequences of your serotype A, the algoritms will reintroduce the gaps, and this way, you will only have to run one alignment.
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The Geneious free trial version still has a lot of useful functionality that might be worth investigating. I used it at home for quite a while, though I was able to go in to the local University when use of a pro version was needed.
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This can be easily accomplished on your desktop.
My experience is with software on Windows so it pertains to that. I use BioEdit to do this kind of analysis. You can set up your genome sequence as a database and your gene sequences as a query and run a local blast or clustalw if that is what you want. If you are looking for mapping coordinates of gene A in the new genome just change your output in Blast to text based which you can import into Excel and analyze.
If you are on a Mac, you can try running BioEdit via Parallels.
My two cents
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