[EMBOSS] Help to build a motif for fzzpro
Hi all, I have been asked to build a motif and the first part of the motif is. "The first 4 AAs must not be acidic and 1 of them should be basic" I am not sure how to do this. So far I have {DE}(4) I am thinking I run with this and then post-filter the fuzzpro file? Any ideas greatfully accepted. Cheers Aengus NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Help to build a motif for fzzpro
Hello Angus, you could use preg with following pattern as written in regular expressions: ([KRH][^DE][^DE][^DE])|([^DE][KRH][^DE][^DE])|([^DE][^DE][KRH][^DE])|([^DE][^DE][^DE][KRH]) Alternatively you could search with four different PROSITE-style patterns using fuzzpro and combine the result tables: [KRH]{DE}(3) {DE}(1)[KRH]{DE}(2) {DE}(2)[KRH]{DE}(1) [KRH]{DE}(3) For searching with combinations of PROSITE patterns, amino acid compositions and eventually AAINDEX profiles we had made a free web application for the University of Oslo, the SAPA tool: http://sapa-tool.uio.no/sapa/index.php E.g. searching a 4-letter subsequence with the PROSITE-style patterns "[KRH].{DE}(4)", where the dot operator means logical AND, will produce a list of all subsequences having the two patterns in that application. Maybe the possibility to combine more than one PROSITE-style pattern within a fuzzpro search with logical AND would be a useful extension for fuzzpro improvement. Often more than one pattern is given for a domain or functional site in the PROSITE pattern database. Of course preg will do the job, however, the PROSITE patterns have to be rewritten as regular expressions. Best regards, Josef Josef Maier, IStLS Information Services to Life Science > Date: Thu, 18 Oct 2012 15:52:44 +0100 > From: Aengus Stewart > Subject: [EMBOSS] Help to build a motif for fzzpro > To: emboss@lists.open-bio.org > Message-ID: <508017bc.80...@cancer.org.uk> > Content-Type: text/plain; charset="ISO-8859-1"; format=flowed > > Hi all, > > I have been asked to build a motif and the first part of the motif > is. > > "The first 4 AAs must not be acidic and 1 of them should be basic" > > I am not sure how to do this. So far I have > > {DE}(4) > > I am thinking I run with this and then post-filter the fuzzpro file? > > > Any ideas greatfully accepted. > > > Cheers > Aengus > > > NOTICE AND DISCLAIMER > This e-mail (including any attachments) is intended for the > above-named person(s). If you are not the intended recipient, notify > the sender immediately, delete this email from your system and do not > disclose or use for any purpose. > > We may monitor all incoming and outgoing emails in line with current > legislation. We have taken steps to ensure that this email and > attachments are free from any virus, but it remains your > responsibility to ensure that viruses do not adversely affect you. > Cancer Research UK Registered charity in England and Wales (1089464), > Scotland (SC041666) and the Isle of Man (1103) A company limited by > guarantee. Registered company in England and Wales (4325234) and the > Isle of Man (5713F). Registered Office Address: Angel Building, 407 St > John Street, London EC1V 4AD. ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Help to build a motif for fzzpro
Dear Aengus, I have an idea of how to do it. You must of course complete the motif/pattern as much as possible because with just {DE}(4) you will find much to much unless you search only a few sequences. You must run the program fuzzpro with parameter -rformat=listfile. You will obtain as output an EMBOSS list file. You can then run fuzzpro again with as sequence input list::xxx (xxx the name of your file) and as pattern input @yyy where yyy contains : > basic_1 <[HKR]. > basic_2 basic_3 basic_4 Indeed, the input will contain only sequence fragments matching the pattern and the basic amino acid hence should be in one of the first 4 positions. Regards, Guy Bottu, ex-collaborator of the Belgian EMBnet Node ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Help to build a motif for fzzpro
On 19/10/2012 10:33, Dr. Josef Maier - IStLS wrote: Hello Angus, you could use preg with following pattern as written in regular expressions: ([KRH][^DE][^DE][^DE])|([^DE][KRH][^DE][^DE])|([^DE][^DE][KRH][^DE])|([^DE][^DE][^DE][KRH]) Alternatively you could search with four different PROSITE-style patterns using fuzzpro and combine the result tables: [KRH]{DE}(3) {DE}(1)[KRH]{DE}(2) {DE}(2)[KRH]{DE}(1) [KRH]{DE}(3) You can also put the four patterns in a file and use the syntax -pattern @patternfile % cat patternfile >first [KRH]{DE}(3) >second {DE}(1)[KRH]{DE}(2) >third {DE}(2)[KRH]{DE}(1) >fourth [KRH]{DE}(3) For searching with combinations of PROSITE patterns, amino acid compositions and eventually AAINDEX profiles we had made a free web application for the University of Oslo, the SAPA tool: http://sapa-tool.uio.no/sapa/index.php Interesting. I'll take a look. E.g. searching a 4-letter subsequence with the PROSITE-style patterns "[KRH].{DE}(4)", where the dot operator means logical AND, will produce a list of all subsequences having the two patterns in that application. Maybe the possibility to combine more than one PROSITE-style pattern within a fuzzpro search with logical AND would be a useful extension for fuzzpro improvement. Often more than one pattern is given for a domain or functional site in the PROSITE pattern database. Of course preg will do the job, however, the PROSITE patterns have to be rewritten as regular expressions. We also have a long standing offer to revive scrutineer, written by Peter Sibbald at EMBL some years ago but it would need translation from Pascal (not too hard to do). It loaded SwissProt into memory and had interesting ways to search for motif patterns. regards, Peter Rice EMBOSS Team ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss