{"action":"created","issue":{"url":"https://api.github.com/repos/DCGenomics/seqr/issues/19","labels_url":"https://api.github.com/repos/DCGenomics/seqr/issues/19/labels{/name}","comments_url":"https://api.github.com/repos/DCGenomics/seqr/issues/19/comments","events_url":"https://api.github.com/repos/DCGenomics/seqr/issues/19/events","html_url":"https://github.com/DCGenomics/seqr/issues/19","id":100404295,"number":19,"title":"DNA Searching","user":{"login":"averagehat","id":5606168,"avatar_url":"https://avatars.githubusercontent.com/u/5606168?v=3","gravatar_id":"","url":"https://api.github.com/users/averagehat","html_url":"https://github.com/averagehat","followers_url":"https://api.github.com/users/averagehat/followers","following_url":"https://api.github.com/users/averagehat/following{/other_user}","gists_url":"https://api.github.com/users/averagehat/gists{/gist_id}","starred_url":"https://api.github.com/users/averagehat/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/averagehat/subscriptions","organizations_url":"https://api.github.com/users/averagehat/orgs","repos_url":"https://api.github.com/users/averagehat/repos","events_url":"https://api.github.com/users/averagehat/events{/privacy}","received_events_url":"https://api.github.com/users/averagehat/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-08-11T20:40:57Z","updated_at":"2015-08-13T12:51:54Z","closed_at":null,"body":"From Lewis:\r\n>There are a couple of approaches to DNA searching we could take with SEQR.  One is to do a translating blastx type search that takes a DNA sequence, converts it to 6 possible protein sequences through a 6 frame translation, then uses these protein sequences to do a search against known protein sequences.  This is a nice approach as if there is a good protein hit, you can be relatively assured that your DNA does translate into a protein in nature.  Protein searches also tend to be more sensitive.\r\n\r\nThat is already in progress [here](https://github.com/DCGenomics/seqr/blob/0bc1265c7f21d1d747738475ff04d0bca37e5d15/src/main/java/gov/nih/nlm/ncbi/seqr/nuc/DNASequenceStreamMap.java)\r\n\r\n>The other approach is to do a straight DNA to DNA search.  We need to do a bit of research on this, but it is uncomplicated.  The only tricky bit is that DNA sequences can be as large as a chromosome, so you need to incorporate some locality in the search.  Fortunately, this is quite easy to do.\r\n\r\nThis would let a lot of people use seqr as a drop-in replacement\r\n"},"comment":{"url":"https://api.github.com/repos/DCGenomics/seqr/issues/comments/130658420","html_url":"https://github.com/DCGenomics/seqr/issues/19#issuecomment-130658420","issue_url":"https://api.github.com/repos/DCGenomics/seqr/issues/19","id":130658420,"user":{"login":"DCGenomics","id":5738421,"avatar_url":"https://avatars.githubusercontent.com/u/5738421?v=3","gravatar_id":"","url":"https://api.github.com/users/DCGenomics","html_url":"https://github.com/DCGenomics","followers_url":"https://api.github.com/users/DCGenomics/followers","following_url":"https://api.github.com/users/DCGenomics/following{/other_user}","gists_url":"https://api.github.com/users/DCGenomics/gists{/gist_id}","starred_url":"https://api.github.com/users/DCGenomics/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DCGenomics/subscriptions","organizations_url":"https://api.github.com/users/DCGenomics/orgs","repos_url":"https://api.github.com/users/DCGenomics/repos","events_url":"https://api.github.com/users/DCGenomics/events{/privacy}","received_events_url":"https://api.github.com/users/DCGenomics/received_events","type":"User","site_admin":false},"created_at":"2015-08-13T12:51:54Z","updated_at":"2015-08-13T12:51:54Z","body":"This is great!  You guys are awesome!\n\nAnother big use case is to search metagenomes (in SRA) for viruses.\n\nSome seminal work (these folks did not get nearly as far with their project\nas you did) is outlined here:\n\nhttps://github.com/DCGenomics/hackathon_v001_metagenomics\n\nCheers!\n\nBen\n\nOn Thu, Aug 13, 2015 at 2:03 AM, lewisg-ncbi <notifications@github.com>\nwrote:\n\n> Hi Paul,\n>\n> Yes absolutely! We should aim to do the translating search (blastx) as\n> it's easy to do.\n>\n> Best,\n> Lewis\n> ________________________________________\n> From: Cutf1 Rmrf [notifications@github.com]\n> Sent: Wednesday, August 12, 2015 11:49 PM\n> To: DCGenomics/seqr\n> Subject: Re: [seqr] DNA Searching (#19)\n>\n> SEQR team,\n>\n> Yes, this would be super cool as one who uses a BLAST pipeline for\n> annotation of viral metagenomes. I had to ditch BLASTX in favor of\n> Rapsearch<https://github.com/zhaoyanswill/RAPSearch2> since BX became way\n> to slow for annotation of thousands of sequences. Even BLASTN (mega) is\n> starting to feel slow.\n>\n> Will there be an announcement when a beta version of SEQR is ready for\n> user testing? I'd love to see how it compares.\n>\n> Thank you,\n>\n> Paul\n>\n> �\n> Reply to this email directly or view it on GitHub<\n> https://github.com/DCGenomics/seqr/issues/19#issuecomment-130521651>.\n>\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/DCGenomics/seqr/issues/19#issuecomment-130548780>.\n>\n\n\n\n-- \nWhat have you done today to make the world a better place?\n"}}