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Recent Activity
Custom Database - HELP?
| Link to this post | posted 26 Apr, 2016 21:24 | |
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Is anyone out there able to add our final annotated sequences to a custom database with all PhagesDB sequences. We would like to do a Phamerator alignment using our finished sequences prior to QC. If it's not too challenging for someone with a small bit of computer knowledge, please give me some ideas of how to go about doing it. I think it would be handy for the future and future annotators too. Thanks. Greg |
| Link to this post | posted 27 Apr, 2016 01:03 | |
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Greg - are you just trying to align with similar phage? You can do that pretty simply by creating a small database and using the web-based tool that was mentioned previously in the forum. You can also do a similar gene length alignment using DNA Master and the Genome Comparison tool with a few select phages for comparison. Would either of these accomplish you overall goal? Putting together a custom Phamerator database for all the phages is a pretty large job. Lee |
| Link to this post | posted 27 Apr, 2016 13:46 | |
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Thanks Lee. Are you taking about the one mentioned in this thread (which I forgot about)? http://seaphages.org/forums/topic/104/ |
| Link to this post | posted 27 Apr, 2016 16:03 | |
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Yes - that is it. It is really good for making small custom databases (I've used it to look at just Streptomyces genomes). I don't think you'd want to use it for a full database though because that would take quite a long time and use a lot of computing resources. Lee |
| Link to this post | posted 27 Apr, 2016 16:05 | |
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Lee HughesThanks! gf |