{"action":"created","issue":{"url":"https://api.github.com/repos/eppic-team/eppic/issues/46","labels_url":"https://api.github.com/repos/eppic-team/eppic/issues/46/labels{/name}","comments_url":"https://api.github.com/repos/eppic-team/eppic/issues/46/comments","events_url":"https://api.github.com/repos/eppic-team/eppic/issues/46/events","html_url":"https://github.com/eppic-team/eppic/issues/46","id":73584255,"number":46,"title":"Find a faster blast alternative","user":{"login":"josemduarte","id":6000474,"avatar_url":"https://avatars.githubusercontent.com/u/6000474?v=3","gravatar_id":"","url":"https://api.github.com/users/josemduarte","html_url":"https://github.com/josemduarte","followers_url":"https://api.github.com/users/josemduarte/followers","following_url":"https://api.github.com/users/josemduarte/following{/other_user}","gists_url":"https://api.github.com/users/josemduarte/gists{/gist_id}","starred_url":"https://api.github.com/users/josemduarte/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josemduarte/subscriptions","organizations_url":"https://api.github.com/users/josemduarte/orgs","repos_url":"https://api.github.com/users/josemduarte/repos","events_url":"https://api.github.com/users/josemduarte/events{/privacy}","received_events_url":"https://api.github.com/users/josemduarte/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/eppic-team/eppic/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":15,"created_at":"2015-05-06T10:29:58Z","updated_at":"2015-10-27T16:07:15Z","closed_at":null,"body":"[transferred from [JIRA](https://jira-bsse.ethz.ch/browse/CRK-138)]\r\n\r\nBlast is very good but slow, especially for our kind of usage where we don't care about sensitivity so much (we look for >50% id homologs). \r\n\r\nSome alternatives are around:\r\n\r\n- [SANS](http://www.ncbi.nlm.nih.gov/pubmed/22962464) and [SANSparallel]( http://nar.oxfordjournals.org/content/early/2015/04/08/nar.gkv317.full) by Liisa Holm\r\n- [USEARCH](http://drive5.com/usearch/) (commercial) \r\n- [BLAT](https://genome.ucsc.edu/FAQ/FAQblat.html#blat3) from UCSC. They also have a [commercial](http://www.kentinformatics.com/products.html) version of it\r\n\r\nSANSparallel looks very promising, the [server](http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi) is incredibly fast."},"comment":{"url":"https://api.github.com/repos/eppic-team/eppic/issues/comments/151552762","html_url":"https://github.com/eppic-team/eppic/issues/46#issuecomment-151552762","issue_url":"https://api.github.com/repos/eppic-team/eppic/issues/46","id":151552762,"user":{"login":"josemduarte","id":6000474,"avatar_url":"https://avatars.githubusercontent.com/u/6000474?v=3","gravatar_id":"","url":"https://api.github.com/users/josemduarte","html_url":"https://github.com/josemduarte","followers_url":"https://api.github.com/users/josemduarte/followers","following_url":"https://api.github.com/users/josemduarte/following{/other_user}","gists_url":"https://api.github.com/users/josemduarte/gists{/gist_id}","starred_url":"https://api.github.com/users/josemduarte/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josemduarte/subscriptions","organizations_url":"https://api.github.com/users/josemduarte/orgs","repos_url":"https://api.github.com/users/josemduarte/repos","events_url":"https://api.github.com/users/josemduarte/events{/privacy}","received_events_url":"https://api.github.com/users/josemduarte/received_events","type":"User","site_admin":false},"created_at":"2015-10-27T16:07:15Z","updated_at":"2015-10-27T16:07:15Z","body":"@sbliven well it's a long story (and a long thread, sorry for the spam). With the new lambda version (0.9.1) things are much better than they used to be in the first posts of this thread. They've introduced a new radix algo that has much lower RAM requirements. After talking to the developers they estimate we'd need 150GB to index a current UniRef100. I'm going to try that out if I can get hold of such a machine around here. You are right in any case that with the skew algo we could do it if we had a very large disk but also a lot of memory (~ 50GB or more). We couldn't do it with the available machines at PSI because we didn't have both of the requirements in one box.\r\n\r\nAbout the 2 use-cases that you give above:\r\n\r\n1. If we really can get the memory, the indexing runs in a few hours so that's not an issue and compares well to the time that blast requires to index (also a few hours). A possibility is also that someone somewhere provides monthly updated precomputed indices so that we all don't have to redo them. At the moment the lambda people provide the index of a ~ 2 months old Uniref, but they are not keeping it up to date (at least yet).\r\n2. Time to query a single sequence is dominated indeed by reading the index file (a minute or more). __However__ they have now implemented (lambda 0.9.1) a shared memory approach (mmapped IO) that apparently is able to share the same index across different instances of the program. That comes close to a client-server architecture where the server is in the background holding the index in memory and the client sends queries that take very little time. Hopefully the full client-server thing comes with new versions."}}