From thomas.bock at embl.de Tue Apr 1 09:55:25 2014 From: thomas.bock at embl.de (Thomas Bock) Date: Tue, 01 Apr 2014 09:55:25 +0200 Subject: [Inparanoid] add species to list Message-ID: <533A70ED.1040602@embl.de> Dear inparanoid team, I would like to find orthologs between human and the species Chaetomium thermophilum. Is it possible to add this species to the gene search list? The genome of Chaetomium thermophilum was published in 2011, here is the link to the publication: http://www.cell.com/abstract/S0092-8674%2811%2900714-8 Kind regards, Thomas Bock -- Thomas Bock (PhD) Postdoctoral Fellow (EIPOD) European Molecular Biology Laboratory (EMBL) Meyerhofstrasse 1 69117 Heidelberg Germany Tel. +49 6221 387 8107 Fax. +49 6221 387 8519 Email: thomas.bock at embl.de From pkastrit at gmail.com Tue Apr 1 11:43:02 2014 From: pkastrit at gmail.com (Panagiotis L. Kastritis) Date: Tue, 1 Apr 2014 11:43:02 +0200 Subject: [Inparanoid] orthologs for chaetomium thermophilum Message-ID: Dear Prof. Erik Sonnhammer, My name is Panagiotis Kastritis and I am a post-doc researcher in EMBL-Heidelberg. I went through your inparanoid database with great interest and I am very happy that such a resource exists for the community. I am working on the organism *Chaetomium thermophilum* (*Chaetomium thermophilum* (strain DSM 1495 / CBS 144.50 / IMI 039719)), and its genome has been published quite recently (Almacher et al, Cell 2011 - PUBMED ID: 21784248). As a consequence 7182 entries exist in Uniprot but ortholog mapping is, unfortunately, not present in your current database version. I would be deeply interesting in mapping orthologs of this organism to those from other eukaryotes, as you have done in your database for all these organisms. Can you suggest me a way on how to do that or whether you plan to update the database in the near future. Thank you very much for the time you spent on my question, Kind Regards, Panos -- __________________________________ Dr. Panagiotis L. Kastritis European Molecular Biology Laboratory e-mail: panagiotis.kastritis at embl.de _________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Tue Apr 1 11:55:40 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Tue, 01 Apr 2014 11:55:40 +0200 Subject: [Inparanoid] orthologs for chaetomium thermophilum In-Reply-To: References: Message-ID: <533A8D1C.2090206@scilifelab.se> Hi, we don't have any plans to make a new Inparanoid release this year. The species included in release 8 were taken from the UniProt complete proteomes, so probably your species was not there. To run inparanoid between human and Chaetomium only takes half a day though, so I recommend you do that. Bests Erik Sonnhammer On 04/01/2014 09:55 AM, Thomas Bock wrote: > Dear inparanoid team, > > I would like to find orthologs between human and the species Chaetomium > thermophilum. Is it possible to add this species to the gene search list? > The genome of Chaetomium thermophilum was published in 2011, here is the > link to the publication: > http://www.cell.com/abstract/S0092-8674%2811%2900714-8 > > Kind regards, > Thomas Bock On 04/01/2014 11:43 AM, Panagiotis L. Kastritis wrote: > Dear Prof. Erik Sonnhammer, > > My name is Panagiotis Kastritis and I am a post-doc researcher in EMBL-Heidelberg. I went through your inparanoid database with great interest and I am very happy that such a resource exists for the community. > > I am working on the organism/Chaetomium thermophilum/ (/Chaetomium thermophilum/ (strain DSM 1495 / CBS 144.50 / IMI 039719)), and its genome has been published quite recently (Almacher et al, Cell 2011 - PUBMED ID: 21784248). As a consequence 7182 entries exist in Uniprot but ortholog mapping is, unfortunately, not present in your current database version. > I would be deeply interesting in mapping orthologs of this organism to those from other eukaryotes, as you have done in your database for all these organisms. > Can you suggest me a way on how to do that or whether you plan to update the database in the near future. > > Thank you very much for the time you spent on my question, > > Kind Regards, > > Panos > > -- > __________________________________ > > Dr. Panagiotis L. Kastritis > European Molecular Biology Laboratory > e-mail: panagiotis.kastritis at embl.de > _________________________________ > > > _______________________________________________ > InParanoid mailing list > InParanoid at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From junwang at unomaha.edu Sat Apr 26 20:10:52 2014 From: junwang at unomaha.edu (Jun Wang) Date: Sat, 26 Apr 2014 18:10:52 +0000 Subject: [Inparanoid] orthologous gene assign Message-ID: Hi, I am now dealing with the comparative genomic project, I want to do orthologous analysis, so I use this inparanoid4.1 software, and it is good. While my problem is: I have more than two species, for example, I have four species (A, B, C, D), how can do it with inparanoid software in order to have the orthologous gene among the four species. Should I do like this (AB, AC, AD, BC, BD, CD)? And then extract the orthologous gene name manually? Thank you very much, I really appreciate it! Bests, Jun Wang University of Nebraska at Omaha -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Mon Apr 28 17:15:52 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Mon, 28 Apr 2014 17:15:52 +0200 Subject: [Inparanoid] orthologous gene assign In-Reply-To: References: Message-ID: <535E70A8.1040901@scilifelab.se> Hi Jun, If the 4 species are "evolutionarily equidistant" from each other, then you can try to use MultiParanoid, http://multiparanoid.sbc.su.se/ Also Hieranoid http://hieranoid.sbc.su.se/ may work, but we acknowledge that Hieranoid has some issues with accuracy at the moment. Bests Erik Sonnhammer On 04/26/2014 08:10 PM, Jun Wang wrote: > > Hi, > > I am now dealing with the comparative genomic project, I want to do > orthologous analysis, so I use this inparanoid4.1 software, and it is > good. While my problem is: I have more than two species, for example, > I have four species (A, B, C, D), how can do it with inparanoid > software in order to have the orthologous gene among the four species. > Should I do like this (AB, AC, AD, BC, BD, CD)? And then extract the > orthologous gene name manually? Thank you very much, I really > appreciate it! > > Bests, > > Jun Wang > > University of Nebraska at Omaha > > > > _______________________________________________ > InParanoid mailing list > InParanoid at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From yutakajr at iq.usp.br Tue Apr 29 13:12:28 2014 From: yutakajr at iq.usp.br (Milton Y. Nishiyama Jr.) Date: Tue, 29 Apr 2014 08:12:28 -0300 Subject: [Inparanoid] InParanoid Digest, Vol 12, Issue 2 In-Reply-To: References: Message-ID: Hi Erik, I would like to know what kind of accuracy issue the hieranoid has, because I'm using it over 6 species not exactly equidistant and I would like to know if there something that I would need to worry about it ? I'm doing the analysis for grass plant species sugarcane, sorghum, rice, maize, panicum, estaria and brachypodium Thank You Milton Em 29/04/2014 07:00, escreveu: > Send InParanoid mailing list submissions to > inparanoid-at-sbc.su.se at lists.su.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se > or, via email, send a message with subject or body 'help' to > inparanoid-at-sbc.su.se-request at lists.su.se > > You can reach the person managing the list at > inparanoid-at-sbc.su.se-owner at lists.su.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of InParanoid digest..." > > > Today's Topics: > > 1. orthologous gene assign (Jun Wang) > 2. Re: orthologous gene assign (Erik Sonnhammer) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 26 Apr 2014 18:10:52 +0000 > From: Jun Wang > To: "inparanoid at sbc.su.se" > Subject: [Inparanoid] orthologous gene assign > Message-ID: > < > eb107523f4624a4680019ec725b878c7 at BLUPR07MB849.namprd07.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > Hi, > I am now dealing with the comparative genomic project, I want to do > orthologous analysis, so I use this inparanoid4.1 software, and it is good. > While my problem is: I have more than two species, for example, I have four > species (A, B, C, D), how can do it with inparanoid software in order to > have the orthologous gene among the four species. Should I do like this > (AB, AC, AD, BC, BD, CD)? And then extract the orthologous gene name > manually? Thank you very much, I really appreciate it! > > Bests, > > Jun Wang > University of Nebraska at Omaha > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20140426/a7a353c4/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Mon, 28 Apr 2014 17:15:52 +0200 > From: Erik Sonnhammer > To: Jun Wang , "inparanoid at sbc.su.se" > > Subject: Re: [Inparanoid] orthologous gene assign > Message-ID: <535E70A8.1040901 at scilifelab.se> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Jun, > > If the 4 species are "evolutionarily equidistant" from each other, then > you can try to use MultiParanoid, http://multiparanoid.sbc.su.se/ > > Also Hieranoid http://hieranoid.sbc.su.se/ may work, but we acknowledge > that Hieranoid has some issues with accuracy at the moment. > > Bests > Erik Sonnhammer > > On 04/26/2014 08:10 PM, Jun Wang wrote: > > > > Hi, > > > > I am now dealing with the comparative genomic project, I want to do > > orthologous analysis, so I use this inparanoid4.1 software, and it is > > good. While my problem is: I have more than two species, for example, > > I have four species (A, B, C, D), how can do it with inparanoid > > software in order to have the orthologous gene among the four species. > > Should I do like this (AB, AC, AD, BC, BD, CD)? And then extract the > > orthologous gene name manually? Thank you very much, I really > > appreciate it! > > > > Bests, > > > > Jun Wang > > > > University of Nebraska at Omaha > > > > > > > > _______________________________________________ > > InParanoid mailing list > > InParanoid at lists.su.se > > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20140428/39442356/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > InParanoid mailing list > InParanoid at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se > > > End of InParanoid Digest, Vol 12, Issue 2 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Tue Apr 29 14:06:20 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Tue, 29 Apr 2014 14:06:20 +0200 Subject: [Inparanoid] InParanoid Digest, Vol 12, Issue 2 In-Reply-To: References: Message-ID: <535F95BC.4060101@scilifelab.se> Hi Milton, yes I think you need to worry about it. In the Hieranoid paper we benchmarked with OrthoBench, believing this was a good test. But after the paper came out we realised that it only measures sensitivity and not specificity. We have recently done some specificity tests and here Hieranoid performs significantly worse than InParanoid, i.e. it has many more false positives. Unfortunately nobody has worked on Hieranoid since the paper came out so we have not resolved this yet, but a new graduate student has just picked up the thread so we hope to be able to fix it soonish. We still don't know what the problem is, so I can't give any estimates of how long it may take. Yours Erik Sonnhammer On 04/29/2014 01:12 PM, Milton Y. Nishiyama Jr. wrote: > > Hi Erik, > > I would like to know what kind of accuracy issue the hieranoid has, > because I'm using it over 6 species not exactly equidistant and I > would like to know if there something that I would need to worry about > it ? > I'm doing the analysis for grass plant species sugarcane, sorghum, > rice, maize, panicum, estaria and brachypodium > > Thank You > > Milton > > Em 29/04/2014 07:00, > escreveu: > > Send InParanoid mailing list submissions to > inparanoid-at-sbc.su.se at lists.su.se > > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se > or, via email, send a message with subject or body 'help' to > inparanoid-at-sbc.su.se-request at lists.su.se > > > You can reach the person managing the list at > inparanoid-at-sbc.su.se-owner at lists.su.se > > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of InParanoid digest..." > > > Today's Topics: > > 1. orthologous gene assign (Jun Wang) > 2. Re: orthologous gene assign (Erik Sonnhammer) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 26 Apr 2014 18:10:52 +0000 > From: Jun Wang > > To: "inparanoid at sbc.su.se " > > > Subject: [Inparanoid] orthologous gene assign > Message-ID: > > > > > Content-Type: text/plain; charset="us-ascii" > > Hi, > I am now dealing with the comparative genomic project, I want to > do orthologous analysis, so I use this inparanoid4.1 software, and > it is good. While my problem is: I have more than two species, for > example, I have four species (A, B, C, D), how can do it with > inparanoid software in order to have the orthologous gene among > the four species. Should I do like this (AB, AC, AD, BC, BD, CD)? > And then extract the orthologous gene name manually? Thank you > very much, I really appreciate it! > > Bests, > > Jun Wang > University of Nebraska at Omaha > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 2 > Date: Mon, 28 Apr 2014 17:15:52 +0200 > From: Erik Sonnhammer > > To: Jun Wang >, > "inparanoid at sbc.su.se " > > > Subject: Re: [Inparanoid] orthologous gene assign > Message-ID: <535E70A8.1040901 at scilifelab.se > > > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Jun, > > If the 4 species are "evolutionarily equidistant" from each other, > then > you can try to use MultiParanoid, http://multiparanoid.sbc.su.se/ > > Also Hieranoid http://hieranoid.sbc.su.se/ may work, but we > acknowledge > that Hieranoid has some issues with accuracy at the moment. > > Bests > Erik Sonnhammer > > On 04/26/2014 08:10 PM, Jun Wang wrote: > > > > Hi, > > > > I am now dealing with the comparative genomic project, I want to do > > orthologous analysis, so I use this inparanoid4.1 software, and > it is > > good. While my problem is: I have more than two species, for > example, > > I have four species (A, B, C, D), how can do it with inparanoid > > software in order to have the orthologous gene among the four > species. > > Should I do like this (AB, AC, AD, BC, BD, CD)? And then extract the > > orthologous gene name manually? Thank you very much, I really > > appreciate it! > > > > Bests, > > > > Jun Wang > > > > University of Nebraska at Omaha > > > > > > > > _______________________________________________ > > InParanoid mailing list > > InParanoid at lists.su.se > > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > InParanoid mailing list > InParanoid at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se > > > End of InParanoid Digest, Vol 12, Issue 2 > ***************************************** > > > > _______________________________________________ > InParanoid mailing list > InParanoid at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From yutakajr at iq.usp.br Tue Apr 29 14:10:38 2014 From: yutakajr at iq.usp.br (Milton Y. Nishiyama Jr.) Date: Tue, 29 Apr 2014 09:10:38 -0300 Subject: [Inparanoid] InParanoid Digest, Vol 12, Issue 2 In-Reply-To: <535F95BC.4060101@scilifelab.se> References: <535F95BC.4060101@scilifelab.se> Message-ID: Hi Erik, Thank You for your reply, that will be very important in my studies. If you get any news please let me know. Best, Milton On Tue, Apr 29, 2014 at 9:06 AM, Erik Sonnhammer < erik.sonnhammer at scilifelab.se> wrote: > Hi Milton, > > yes I think you need to worry about it. In the Hieranoid paper we > benchmarked with OrthoBench, believing this was a good test. But after the > paper came out we realised that it only measures sensitivity and not > specificity. We have recently done some specificity tests and here > Hieranoid performs significantly worse than InParanoid, i.e. it has many > more false positives. Unfortunately nobody has worked on Hieranoid since > the paper came out so we have not resolved this yet, but a new graduate > student has just picked up the thread so we hope to be able to fix it > soonish. We still don't know what the problem is, so I can't give any > estimates of how long it may take. > > Yours > Erik Sonnhammer > > > On 04/29/2014 01:12 PM, Milton Y. Nishiyama Jr. wrote: > > Hi Erik, > > I would like to know what kind of accuracy issue the hieranoid has, > because I'm using it over 6 species not exactly equidistant and I would > like to know if there something that I would need to worry about it ? > I'm doing the analysis for grass plant species sugarcane, sorghum, rice, > maize, panicum, estaria and brachypodium > > Thank You > > Milton > Em 29/04/2014 07:00, > escreveu: > >> Send InParanoid mailing list submissions to >> inparanoid-at-sbc.su.se at lists.su.se >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se >> or, via email, send a message with subject or body 'help' to >> inparanoid-at-sbc.su.se-request at lists.su.se >> >> You can reach the person managing the list at >> inparanoid-at-sbc.su.se-owner at lists.su.se >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of InParanoid digest..." >> >> >> Today's Topics: >> >> 1. orthologous gene assign (Jun Wang) >> 2. Re: orthologous gene assign (Erik Sonnhammer) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sat, 26 Apr 2014 18:10:52 +0000 >> From: Jun Wang >> To: "inparanoid at sbc.su.se" >> Subject: [Inparanoid] orthologous gene assign >> Message-ID: >> < >> eb107523f4624a4680019ec725b878c7 at BLUPR07MB849.namprd07.prod.outlook.com> >> >> Content-Type: text/plain; charset="us-ascii" >> >> Hi, >> I am now dealing with the comparative genomic project, I want to do >> orthologous analysis, so I use this inparanoid4.1 software, and it is good. >> While my problem is: I have more than two species, for example, I have four >> species (A, B, C, D), how can do it with inparanoid software in order to >> have the orthologous gene among the four species. Should I do like this >> (AB, AC, AD, BC, BD, CD)? And then extract the orthologous gene name >> manually? Thank you very much, I really appreciate it! >> >> Bests, >> >> Jun Wang >> University of Nebraska at Omaha >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20140426/a7a353c4/attachment-0001.html >> > >> >> ------------------------------ >> >> Message: 2 >> Date: Mon, 28 Apr 2014 17:15:52 +0200 >> From: Erik Sonnhammer >> To: Jun Wang , "inparanoid at sbc.su.se" >> >> Subject: Re: [Inparanoid] orthologous gene assign >> Message-ID: <535E70A8.1040901 at scilifelab.se> >> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" >> >> Hi Jun, >> >> If the 4 species are "evolutionarily equidistant" from each other, then >> you can try to use MultiParanoid, http://multiparanoid.sbc.su.se/ >> >> Also Hieranoid http://hieranoid.sbc.su.se/ may work, but we acknowledge >> that Hieranoid has some issues with accuracy at the moment. >> >> Bests >> Erik Sonnhammer >> >> On 04/26/2014 08:10 PM, Jun Wang wrote: >> > >> > Hi, >> > >> > I am now dealing with the comparative genomic project, I want to do >> > orthologous analysis, so I use this inparanoid4.1 software, and it is >> > good. While my problem is: I have more than two species, for example, >> > I have four species (A, B, C, D), how can do it with inparanoid >> > software in order to have the orthologous gene among the four species. >> > Should I do like this (AB, AC, AD, BC, BD, CD)? And then extract the >> > orthologous gene name manually? Thank you very much, I really >> > appreciate it! >> > >> > Bests, >> > >> > Jun Wang >> > >> > University of Nebraska at Omaha >> > >> > >> > >> > _______________________________________________ >> > InParanoid mailing list >> > InParanoid at lists.su.se >> > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20140428/39442356/attachment-0001.html >> > >> >> ------------------------------ >> >> _______________________________________________ >> InParanoid mailing list >> InParanoid at lists.su.se >> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se >> >> >> End of InParanoid Digest, Vol 12, Issue 2 >> ***************************************** >> > > > _______________________________________________ > InParanoid mailing listInParanoid at lists.su.sehttps://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se > > > -- ================================================= Milton Yutaka Nishiyama Jr. PhD Student Bioinformatics Group - IME/IQ - USP Biochemistry Department, University of Sao Paulo http://sucest-fun.org/ Brazil ================================================= -------------- next part -------------- An HTML attachment was scrubbed... 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