[Inparanoid] InParanoid Digest, Vol 12, Issue 2

Tue Apr 29 14:10:38 CEST 2014

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, <inparanoid-at-sbc.su.se-request at lists.su.se>
> 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 <junwang at unomaha.edu>
>> To: "inparanoid at sbc.su.se" <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 <erik.sonnhammer at scilifelab.se>
>> To: Jun Wang <junwang at unomaha.edu>,     "inparanoid at sbc.su.se"
>>         <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...
URL: <http://lists.su.se/pipermail/inparanoid-at-sbc.su.se/attachments/20140429/183184d8/attachment.html>