From owner-bio-srs@hgmp.mrc.ac.uk Tue Jan 7 12:20:28 2003 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id D174C7D272 for ; Tue, 7 Jan 2003 12:20:28 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 4DF007D27F for ; Tue, 7 Jan 2003 12:20:28 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 90AF57D272; Tue, 7 Jan 2003 12:20:21 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2942C7D1F4 for ; Mon, 16 Dec 2002 16:13:20 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 0F7AD7D221; Mon, 16 Dec 2002 16:13:14 +0000 (GMT) To: bionet-software-srs@net.bio.net From: gene.quantification@wzw.tum.de (Gene Quantification Homepage) Newsgroups: bionet.software.srs Subject: Gene Quantification Newsletter X-mas 2002 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <5.0.2.1.0.20021216171848.02e8cca0@pollux.wzw.tum.de> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_31104859==_.ALT" X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 468EE7D21B; Mon, 16 Dec 2002 16:13:13 +0000 (GMT) X-Received: from pollux.wzw.tum.de (pollux.edv.agrar.tu-muenchen.de [141.40.103.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 374FC7D1F4; Mon, 16 Dec 2002 16:13:10 +0000 (GMT) X-Received: from pfaffl.wzw.tum.de ([141.40.217.71]) by pollux.wzw.tum.de (AIX4.3/8.9.3/8.9.3) with ESMTP id RAA34590; Mon, 16 Dec 2002 17:13:09 +0100 X-Sender: genequan@pollux.wzw.tum.de X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 X-To: bio-srs@net.bio.net, bionauts@net.bio.net, cellbiol@net.bio.net, immuno@net.bio.net Date: Tue, 7 Jan 2003 12:20:21 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk --=====================_31104859==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Gene Quantification Newsletter X-mas 2002 December 2002 Merry Christmas and a happy New Year To all Newsletter Readers and Gene Quantification Visitors NEW features: Determination of real-time PCR efficiency NEW EQUATIONS & ALGORITHMS by Tichopad et al. 2002 http://www.wzw.tum.de/gene-quantification/efficiency.html#e-fluoro-sig-2 and http://www.wzw.tum.de/gene-quantification/efficiency.html Endocrinology & Mammary Gland Immunology - NEW PUBLICATIONS http://www.wzw.tum.de/gene-quantification/physiology.shtml Steroid receptors: AR, ERa, ERb, PR Adrenergic receptors: alpha-1-subtypes & alpha-2-subtypes & beta-subtypes Somatotropic axis: GHR, IGF-1, IGF2, both IGF receptors & IGF-BP1 to BP3 Serotonin receptors (coming soon) NEW MOVIES http://www.wzw.tum.de/gene-quantification/movie.html e.g. Molecular Biology, PCR, RPA, Electrophoresis, Northern- & Southern-Blot NEW PUBLICATIONS about kinetic PCR http://www.wzw.tum.de/gene-quantification/real-time.html and http://www.wzw.tum.de/gene-quantification/chemistry.html and http://www.wzw.tum.de/gene-quantification/hkg.html and http://www.wzw.tum.de/gene-quantification/literature.html Poster boards (a little bit slow !!!): http://www.wzw.tum.de/gene-quantification/poster-a.html methodological poster board A: Array verification physiological poster board B: IGFs - Early Response Genes physiological poster board C: Steroid receptors physiological poster board D: Zinc metabolism physiological poster board E: Immunological relevant factors New links & databases: http://www.wzw.tum.de/gene-quantification/link.html http://www.realtimeprimerdatabase.ht.st http://www.realtimeprimers.org/ http://www.pcrlinks.com http://www.pcrlinks.com/variants/real-time_pcr.htm http://www.cyclertest.com/ The COMPLETE Alkami Quick GuideTM for PCR is a (158 pages) http://www.wzw.tum.de/gene-quantification/quick-guide-pcr.pdf EUROGENTEC PCR manual (48 pages) http://www.wzw.tum.de/gene-quantification/eurogentec-qq-booklet.pdf LightCycler University (LCU) http://www.wzw.tum.de/gene-quantification/real-time.html#lcu Please send the NEWSLETTER and the home page links to further scientists and friends who are interested in real-time PCR, new quantification strategies, relative or absolute gene quantification using kinetic PCR. best regards Michael Pfaffl ############################################# For further QUESTIONS concerning real-time PCR and if you want to SUBSCRIBE to our monthly appearing GENE QUANTIFICATION NEWSLETTER please contact gene.quantification@wzw.tum.de You will receive all NEW FEATURES and future REST & REST-XL updates. GENE QUANTIFICATION web page and the GENE QUANTIFICATION NEWSLETTER are non-commercial, educational sites with the only purpose of facilitating access to biology-related information over the internet. The web page is optimised for Netscape Navigator version 4.7 & Internet Explorer version 5.0 (and higher versions) with an optimal screen resolution of 1024 x 768 pixels. GENE QUANTIFICATION web page visits and DOWNLOAD statistics are listed here: http://www.wzw.tum.de/gene-quantification/contact.html#server If you want UN-SUBSCRIBE from all future NEWSLETTERS please contact gene.quantification@wzw.tum.de and type REMOVE into the subject line. You will be removed instantly from our mailing list. ******************************************************************** Gene Quantification @ wzw.tum.de e-mail: gene.quantification@wzw.tum.de homepage: http://www.wzw.tum.de/gene-quantification/index.shtml homepage: http://www.wzw.tum.de/gene-quantification/physiology.shtml responsible Senior Scientist: Dr. Michael W. Pfaffl Institute of Physiology Life Science Center Weihenstephan, Technical University of Munich Weihenstephaner Berg 3 D-85350 Freising-Weihenstephan GERMANY ******************************************************************** --=====================_31104859==_.ALT Content-Type: text/html; charset="us-ascii" Gene Quantification Newsletter X-mas 2002
December 2002

Merry Christmas and a happy New Year
To all Newsletter Readers and Gene Quantification Visitors

NEW features:

Determination of real-time PCR efficiency
NEW EQUATIONS & ALGORITHMS by Tichopad et al. 2002
http://www.wzw.tum.de/gene-quantification/efficiency.html#e-fluoro-sig-2
and
http://www.wzw.tum.de/gene-quantification/efficiency.html

Endocrinology & Mammary Gland Immunology - NEW PUBLICATIONS
http://www.wzw.tum.de/gene-quantification/physiology.shtml
Steroid receptors:   AR, ERa, ERb, PR
Adrenergic receptors:   alpha-1-subtypes & alpha-2-subtypes & beta-subtypes
Somatotropic axis:   GHR, IGF-1, IGF2, both IGF receptors & IGF-BP1 to BP3
Serotonin receptors   (coming soon)

NEW MOVIES
http://www.wzw.tum.de/gene-quantification/movie.html
e.g. Molecular Biology, PCR, RPA, Electrophoresis, Northern- & Southern-Blot

NEW PUBLICATIONS about kinetic PCR
http://www.wzw.tum.de/gene-quantification/real-time.html
and
http://www.wzw.tum.de/gene-quantification/chemistry.html
and
http://www.wzw.tum.de/gene-quantification/hkg.html
and
http://www.wzw.tum.de/gene-quantification/literature.html

Poster boards (a little bit slow !!!):
http://www.wzw.tum.de/gene-quantification/poster-a.html
methodological poster board A: Array verification
physiological poster board B:     IGFs - Early Response Genes
physiological poster board C:     Steroid receptors
physiological poster board D:     Zinc metabolism
physiological poster board E:     Immunological relevant factors

New links & databases:
http://www.wzw.tum.de/gene-quantification/link.html
http://www.realtimeprimerdatabase.ht.st
http://www.realtimeprimers.org/
http://www.pcrlinks.com
http://www.pcrlinks.com/variants/real-time_pcr.htm
http://www.cyclertest.com/

The COMPLETE Alkami Quick GuideTM for PCR is a (158 pages)
http://www.wzw.tum.de/gene-quantification/quick-guide-pcr.pdf

EUROGENTEC PCR manual (48 pages)
http://www.wzw.tum.de/gene-quantification/eurogentec-qq-booklet.pdf

LightCycler University (LCU)
http://www.wzw.tum.de/gene-quantification/real-time.html#lcu

Please send the NEWSLETTER and the home page links to further scientists and friends who are interested in real-time PCR, new quantification strategies, relative or absolute gene quantification using kinetic PCR.

best regards

Michael Pfaffl

#############################################

For further QUESTIONS concerning real-time PCR and if you want to SUBSCRIBE to our monthly appearing GENE QUANTIFICATION NEWSLETTER please contact gene.quantification@wzw.tum.de   You will receive all NEW FEATURES and future REST & REST-XL updates.

GENE QUANTIFICATION web page and the GENE QUANTIFICATION NEWSLETTER are non-commercial, educational sites with the only purpose of facilitating access to biology-related information over the internet. The web page is optimised for Netscape Navigator version 4.7 & Internet Explorer version 5.0 (and higher versions) with an optimal screen resolution of 1024 x 768 pixels.

GENE QUANTIFICATION web page visits and DOWNLOAD statistics are listed here: http://www.wzw.tum.de/gene-quantification/contact.html#server

If you want UN-SUBSCRIBE from all future NEWSLETTERS please contact gene.quantification@wzw.tum.de and type REMOVE into the subject line. You will be removed instantly from our mailing list.

********************************************************************
Gene Quantification @ wzw.tum.de

e-mail: gene.quantification@wzw.tum.de
homepage: http://www.wzw.tum.de/gene-quantification/index.shtml
homepage: http://www.wzw.tum.de/gene-quantification/physiology.shtml

responsible Senior Scientist:
Dr. Michael W. Pfaffl
Institute of Physiology
Life Science Center Weihenstephan,
Technical University of Munich
Weihenstephaner Berg 3
D-85350 Freising-Weihenstephan
GERMANY

******************************************************************** --=====================_31104859==_.ALT-- --- From owner-bio-srs@hgmp.mrc.ac.uk Tue Jan 7 12:21:13 2003 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 476BC7D26C for ; Tue, 7 Jan 2003 12:21:13 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id BC93A7D0C7 for ; Tue, 7 Jan 2003 12:21:12 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 5675F7D26C; Tue, 7 Jan 2003 12:20:27 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 11BE47D1E0 for ; Sun, 15 Dec 2002 11:06:35 +0000 (GMT) Received: from smtp10.atl.mindspring.net (smtp10.atl.mindspring.net [207.69.200.246]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 934F37D135 for ; Sun, 15 Dec 2002 11:06:31 +0000 (GMT) Received: from [192.168.163.60] (helo=slb2.atl.mindspring.net) by smtp10.atl.mindspring.net with esmtp (Exim 3.33 #1) id 18NWbI-0007u3-00 for bionet-software-srs@net.bio.net; Sun, 15 Dec 2002 06:06:25 -0500 Received: (from news@localhost) by slb2.atl.mindspring.net (8.8.5/8.7.3) id GAA27415; Sun, 15 Dec 2002 06:06:25 -0500 (EST) To: bionet-software-srs@net.bio.net From: Andrew Dalke Newsgroups: bionet.software.srs Subject: question using SRS's web interface Organization: Dalke Scientific Software, LLC Message-ID: Reply-To: dalke@dalkescientific.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Server-Date: 15 Dec 2002 11:06:25 GMT User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20021130 X-Accept-Language: en-us, en Date: Tue, 7 Jan 2003 12:20:27 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk I'm having some problems understanding how to use the web interface to SRS. I just ran through an Entrex tutorial at http://healthlinks.washington.edu/hsl/liaisons/yarfitz/EntrezTutorial/index.html and decided to use some of the same examples, to get a feel for the differences between SRS and Entrez. I want to get "Nucleotide" record "X61499". With NCBI's ExPASy this returns a single hit, X61499 Links H.sapiens mRNA for NF-kB subunit gi|35041|emb|X61499.1|HSNFKBSU[35041] How do I do the same on an SRS server? I went to srs.ebi.ac.uk to find publically available GenBank servers. That took me to http://downloads.lionbio.co.uk/publicsrs.html I choose IUBIO (19808101), at http://iubio.bio.indiana.edu/srs6bin/cgi-bin/wgetz?-page+LibInfo+-lib+GENBANKRELEASE Then "TOP PAGE" so I could do a query. Select GENBANK and GENPEPT. (Both, to be on the safe side) Enter "X61499" in the "Quick Search" box, and press the "Quick Search" button. Here are the hits: GENBANK:AE015854 <-- because of note "similar to GB:X61498 ..." GENBANK:HSCD85703 <-- don't know why there was a match GENBANK:HSPA18H7 <-- don't know why there was a match GENPEPT:AE015854_2 <-- because of note "similar to GB:X61498, GB:X61499 ..." GENPEPT:X61499_1 <-- contains ACCESSION X61499, so this make sense The last of these links back to GI:35042. (Note that NCBI's link is for GI:35041) I follow the hyperlink to GI:35042 and get no entries found query: "[genbank-GID:35042]" I manually changed the URL to point to 35041 and get .. H.sapiens flow-sorted chromosome 6 HindIII fragment, SC6pA18H7. which is quite wrong. I did a description search for "mRNA for NF-kB subunit". It took a long time (maybe five minutes?) and came back with 4 links. And the descriptions were for: * GENBANK:HSPA18H6 H.sapiens flow-sorted chromosome 6 HindIII fragment, SC6pA18H6. * GENBANK:HSPA18H7 H.sapiens flow-sorted chromosome 6 HindIII fragment, SC6pA18H7. * GENBANK:CRH406200 Carlia rhomboidalis partial mitochondrial cytb gene for cytochrome b, sample CJS700. * GENBANK:CRH406201 Carlia rhomboidalis partial mitochondrial cytb gene for cytochrome b, sample CJS701. Note that one of them matched earlier for X61499. Were I to guess I would say there's an off-by-one error in the index? I then tried Pasteur at http://srs.pasteur.fr/cgi-bin/srs6/wgetz?-page+top+-id+5Ajh91KEYoX Again, GenPept and GenBank quick search for "X61499" GENBANK:AE015854 <-- note about "similar to" GENBANK:BI339638 <-- don't know why this is here GENBANK:BI357633 <-- don't know why this is here GENBANK:AE015854 <-- note about "similar to" GENPEPT:AE015854_2 <-- note about "similar to" GENPEPT:X61499_1 <-- obvious GENPEPT:AE015854_2 <-- note about "similar to" Again, I looked at GENPEPT:X61499_1 to see if there's a link to the nucleotide. It says LOCUS X61499_1 [HSNFKBSU] DEFINITION H.sapiens mRNA for NF-kB subunit. DATE 29-APR-1992 ACCESSION X61499 ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. COMMENT CDS 164..1411 /product="NF-kB subunit" /protein_id="CAA43716.1" /db_xref="GI:35042" /db_xref="SWISS-PROT:Q04860" WEIGHT 45548 LENGTH 415 Note that the /db_xref="GI:35042" has the GI:35042 hyperlinked, so I follow it. The resulting page contains Entry Name GENBANK:BI357633 Accession Number BI357633 NID 15052079 Sequence Version 1 Division EST Molecule mRNA Date 31-JUL-2001 Description Source Drosophila melanogaster (fruit fly) Organism Drosophila melanogaster Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila. Keywords EST Description RE44159.5prime RE Drosophila melanogaster normalized Embryo pFlc-1 Drosophila melanogaster cDNA clone RE44159 5 similar to CG14819: FBan0014819 located on: X 2A3-2A3;: 05/13/2001, mRNA sequence. ... Length: 593 I don't see how a nucleotide of length 593 can make a protein of length 415. I also don't see how the source of a human protein comes from Drosophila. What's going on? Andrew dalke@dalkescientific.com From owner-bio-srs@hgmp.mrc.ac.uk Tue Jan 14 11:27:07 2003 Return-Path: X-Original-To: bio-srs-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 435BA7D29E for ; Tue, 14 Jan 2003 11:27:07 +0000 (GMT) X-Original-To: bio-srs-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id BA2277D287 for ; Tue, 14 Jan 2003 11:27:06 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 6C9607D32F; Tue, 14 Jan 2003 11:27:05 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C8A857D198 for ; Thu, 9 Jan 2003 14:52:13 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id C1D6F7D0C5; Thu, 9 Jan 2003 14:52:12 +0000 (GMT) To: bionet-software-srs@net.bio.net From: bca@nildram.co.uk ("Benedict Arnold") Newsgroups: bionet.software.srs Subject: Re: question using SRS's web interface Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <001901c2b7ee$a4a659a0$fb2f70c3@ben2> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0016_01C2B7EE.A419D110" X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B365E7D100 for ; Thu, 9 Jan 2003 14:52:11 +0000 (GMT) X-Received: from mrburns.nildram.co.uk (mrburns.nildram.co.uk [195.112.4.54]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3FB607D0C5 for ; Thu, 9 Jan 2003 14:52:10 +0000 (GMT) X-Received: from ben2 (ppp47-251.dial.nildram.co.uk [195.112.47.251]) by mrburns.nildram.co.uk (Postfix) with SMTP id B54BC1E1F2D for ; Thu, 9 Jan 2003 14:52:05 +0000 (GMT) X-To: X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Date: Tue, 14 Jan 2003 11:27:05 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk This is a multi-part message in MIME format. ------=_NextPart_000_0016_01C2B7EE.A419D110 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Andrew, I've had a look but can't seem to duplicate the results you get on the = servers named ... I couldn't begin to guess why. In general, due to the way SRS does its' searches, SRS tends to return = more results than Entrez. I suspect this is because Entrez is searching = a more limited selection of fields whereas SRS quick search looks in = indices for all fields that have be created for those databases. This = would explain why you were getting hits that contained "similar to". It is possible that the indices you looked at were corrupt or a newer = version of SRS was installed but the indices (or the virtual query sets = used to create the complete sequence libraries weren't recreated) and = this has lead to the lack of duplication of results and probably those = entries where there is no obvious reason for the hit to be returned ... One reason for the 35041/35042 mismatch is that the genpept entry under = SRS contains GI:35042, this is in the data flatfile so this is the = number used to create the link. The "no entries found" message is = probably returned because this GID number has been removed from genbank = but not updated in genpept so SRS isn't really at fault here, blame the = data as a search for 35042 in Genbank returns nothig as well. It is also possible that the linking indices between Genbank and Genpept = haven't been recreated successfully and thus the links between the two = databases point to the wrong entries or the data needed to create these = links doesn't exist in the data. I hope you don't give up on SRS because it is a very useful system, = albeit, sometimes the results can be confusing given some of the = problems that can occur as outlined above. hope that helps explains some of the problems you've encountered all the best Benedict Arnold ------=_NextPart_000_0016_01C2B7EE.A419D110 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi Andrew,

I've had a look but can't seem to = duplicate the=20 results you get on the servers named ... I couldn't begin to guess=20 why.

In general, due to the way SRS does = its' searches,=20 SRS tends to return more results than Entrez. I suspect this is because = Entrez=20 is searching a more limited selection of fields whereas SRS quick search = looks=20 in indices for all fields that have be created for those databases. This = would=20 explain why you were getting hits that contained "similar = to".

It is possible that the indices you = looked at were=20 corrupt or a newer version of SRS was installed but the indices (or the = virtual=20 query sets used to create the complete sequence libraries = weren't=20 recreated) and this has lead to the lack of duplication of results and = probably=20 those entries where there is no obvious reason for the hit to be = returned=20 ...

One reason for the 35041/35042 = mismatch is=20 that the genpept entry under SRS contains GI:35042, this is in the data = flatfile=20 so this is the number used to create the link. The "no entries found" = message is=20 probably returned because this GID number has been removed from genbank = but not=20 updated in genpept so SRS isn't really at fault here, blame the data as = a search=20 for 35042 in Genbank returns nothig as well.

It is also possible that the linking = indices=20 between Genbank and Genpept haven't been recreated successfully and thus = the=20 links between the two databases point to the wrong entries or the data = needed to=20 create these links doesn't exist in the data.

I hope you don't give up on SRS = because it is=20 a very useful system, albeit, sometimes the results can be confusing = given some=20 of the problems that can occur as outlined above.

hope that helps explains some of the = problems=20 you've encountered

all the best

Benedict Arnold

------=_NextPart_000_0016_01C2B7EE.A419D110-- --- From owner-bio-srs@hgmp.mrc.ac.uk Thu Jan 23 11:38:14 2003 Return-Path: X-Original-To: bio-srs-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 313057D21A for ; Thu, 23 Jan 2003 11:38:14 +0000 (GMT) X-Original-To: bio-srs-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 801DD7D10C for ; Thu, 23 Jan 2003 11:38:13 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 2E34A7D10F; Thu, 23 Jan 2003 11:38:12 +0000 (GMT) X-Original-To: bio-srs-submit@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 580817D1A2 for ; Wed, 22 Jan 2003 14:32:29 +0000 (GMT) Received: from horus.isnic.is (horus.isnic.is [193.4.58.12]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3747D7D152 for ; Wed, 22 Jan 2003 14:32:26 +0000 (GMT) Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by horus.isnic.is (8.12.3/8.12.3/isnic) with ESMTP id h0MEWLtJ089802 for ; Wed, 22 Jan 2003 14:32:25 GMT (envelope-from news@vub.ac.be) Received: from snic.vub.ac.be (snic.ulb.ac.be [164.15.128.20]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id PAA28244; Wed, 22 Jan 2003 15:29:57 +0100 (MET) for Received: (news@localhost) by snic.vub.ac.be (8.9.3/%I%.0.ap (snic.test)) id PAA03203; Wed, 22 Jan 2003 15:31:44 +0100 (MET) for bionet-software-srs@moderators.isc.org To: bionet-software-srs@moderators.isc.org From: Guy Bottu Newsgroups: bionet.software.srs Subject: Re: question using SRS's web interface Organization: Belgian EMBnet Node Message-ID: References: X-Trace: snic.vub.ac.be 1043245904 29844 134.184.15.24 (22 Jan 2003 14:31:44 GMT) X-Complaints-To: usenet@snic.vub.ac.be NNTP-Posting-Date: 22 Jan 2003 14:31:44 GMT User-Agent: tin/1.4.5-20010409 ("One More Nightmare") (UNIX) (OSF1/V5.1 (alpha)) Date: Thu, 23 Jan 2003 11:38:12 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk Dear Andrew, Probably either the databank was not up-to-date or the indexes were not up-to-date (and hence pointing to wrong entries). I know by experience that keeping a server with HUGE databanks up-to-date is hard... I tried, at Indiana it still does not work, at Pasteur and also at our site (http://www.be.embnet.org/srs) you get what you want. GENBANK:AE015854 (similar to) GENBANK:HSBA18I14 (similar to) GENBANK:HSNFKBSU GENPEPT:AE015854_2 (similar to) GENPEPT:X61499_1 Note : if you click on "Standard" or "Extended" you can search specifically for X61499 in the "Accession Number" field. Regards, Guy Bottu From owner-bio-srs@hgmp.mrc.ac.uk Tue Jan 28 09:29:07 2003 Return-Path: X-Original-To: bio-srs-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 65AD07D3A5 for ; Tue, 28 Jan 2003 09:29:07 +0000 (GMT) X-Original-To: bio-srs-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B9CC97D3A1 for ; Tue, 28 Jan 2003 09:29:06 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id B8C6D7D39B; Tue, 28 Jan 2003 09:29:05 +0000 (GMT) X-Original-To: bio-srs-submit@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 3579C7D167 for ; Mon, 27 Jan 2003 17:20:39 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id 582887D0FD; Mon, 27 Jan 2003 17:20:38 +0000 (GMT) To: bionet-software-srs@net.bio.net From: agbiotec@agriroot.aua.gr ("Constantinos G. Crambis") Newsgroups: bionet.software.srs Subject: Extraction of portions of GenBank flatfiles Organization: Agricultural University of Athens Message-ID: <000f01c2c628$605cc840$58df6693@ntua> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0010_01C2C639.23E59840" X-Original-To: bio-srs@hgmp.mrc.ac.uk X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5351E7D167 for ; Mon, 27 Jan 2003 17:20:37 +0000 (GMT) X-Received: from diomedes.noc.ntua.gr (unknown [147.102.222.220]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B18657D0FD for ; Mon, 27 Jan 2003 17:20:35 +0000 (GMT) X-Received: from mail.ntua.gr (mail.ntua.gr [147.102.222.65]) by diomedes.noc.ntua.gr (8.11.6/8.11.6) with ESMTP id h0RHKZ145636 for ; Mon, 27 Jan 2003 19:20:35 +0200 (EET) X-Received: from ntua (ppp088.dialup.ntua.gr [147.102.223.88]) by mail.ntua.gr (Netscape Messaging Server 4.15) with ESMTP id H9DUU400.AO5 for ; Mon, 27 Jan 2003 19:20:28 +0200 X-Reply-To: X-To: X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2616 X-Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Date: Tue, 28 Jan 2003 09:29:05 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk This is a multi-part message in MIME format. ------=_NextPart_000_0010_01C2C639.23E59840 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Is anyone aware of any software (not commercial), that can be used for extraction of portions of the flatfiles ? (I think that's how they call the GenBank entries you get after a search) . For example if in a database flatfile entry, you have a reference to coding sequence as " CDS : 235 ... 1500 bp" , is there a software that can find the keyword "CDS" in the flatfile, and then read and return the string composed of the letters a c g t, that is between the numbers 235...1500 in the sequence at the end of the file ? I am particularly interested, to extract promoter regions from whole gene entries of GenBank. Constantinos G. Crambis Agricultural University of Athens Dept. of Agricultural Biotechnology Molecular Biology Lab agbiotec@agriroot.aua.gr agbiotec@yahoo.com ------=_NextPart_000_0010_01C2C639.23E59840 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Is anyone aware of any software (not commercial), = that can be used for extraction of portions of the

flatfiles ? (I think that’s how they call the GenBank entries you get after a search) . For example if in a database flatfile entry, =

you have a reference to coding sequence as “ CDS : 235 ….. 1500 bp” , is there a software that can find the = keyword “CDS”

in the = flatfile, and then read and return the string = composed of the letters a c g t, that is between the numbers 235…..1500 =

in the = sequence at the end of the file ? I am particularly interested, to extract promoter = regions from whole gene entries of

GenBank= .

Constantinos = G. Crambis

Agricultural = University of = Athens

Dept. of Agricultural = Biotechnology

Molecular Biology = Lab

agbiotec@agriroot.aua.gr

agbiotec@yahoo.com

------=_NextPart_000_0010_01C2C639.23E59840-- --- From owner-bio-srs@hgmp.mrc.ac.uk Tue Jan 28 09:29:16 2003 Return-Path: X-Original-To: bio-srs-outgoing Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with SMTP id 155E27D39B for ; Tue, 28 Jan 2003 09:29:16 +0000 (GMT) X-Original-To: bio-srs-list@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 63E757D3A4 for ; Tue, 28 Jan 2003 09:29:15 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6015) id 763127D39B; Tue, 28 Jan 2003 09:29:13 +0000 (GMT) X-Original-To: bio-srs-submit@hgmp.mrc.ac.uk Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 84F677D356 for ; Mon, 27 Jan 2003 09:46:32 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 60001) id AD8437D35A; Mon, 27 Jan 2003 09:46:28 +0000 (GMT) To: bionet-software-srs@net.bio.net From: gene.quantification@wzw.tum.de (Gene Quantification Homepage) Newsgroups: bionet.software.srs Subject: Gene Quantification Newsletter - January 2003 Organization: BIOSCI/MRC Human Genome Mapping Project Resource Centre Message-ID: <5.0.2.1.0.20030127104513.02fe3aa8@pollux.wzw.tum.de> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_7570171==_.ALT" X-Original-To: bio-srs@hgmp.mrc.ac.uk X-Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 5DDC37D222; Mon, 27 Jan 2003 09:46:26 +0000 (GMT) X-Received: from pollux.wzw.tum.de (pollux.edv.agrar.tu-muenchen.de [141.40.103.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 0C52E7D35A; Mon, 27 Jan 2003 09:46:23 +0000 (GMT) X-Received: from pfaffl.wzw.tum.de ([141.40.217.71]) by pollux.wzw.tum.de (AIX4.3/8.9.3/8.9.3) with ESMTP id KAA33358; Mon, 27 Jan 2003 10:46:21 +0100 X-Sender: genequan@pollux.wzw.tum.de X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 X-To: bio-srs@net.bio.net, bionauts@net.bio.net, cellbiol@net.bio.net, immuno@net.bio.net Date: Tue, 28 Jan 2003 09:29:13 +0000 (GMT) Sender: owner-bio-srs@hgmp.mrc.ac.uk Precedence: bulk --=====================_7570171==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Gene Quantification Newsletter - January 2003 Happy New Year 2003 to all Newsletter Readers and Gene Quantification Visitors NEW features: RNA and Gene Expression - NEW PUBLICATIONS Tissue-specific expression pattern of bovine prion gene (PrP): Quantification using real-time RT-PCR http://www.wzw.tum.de/gene-quantification/absolute.html#prp Detection and quantification of mRNA-expression of alpha- and beta-adrenergic receptor subtypes in the mammary gland of dairy cows. http://www.wzw.tum.de/gene-quantification/endo.html#adrenerg Gene Quantification in Endocrinology - NEW PUBLICATIONS Gene Expression of Immunologically Important Factors in Blood Cells, Milk Cells and Mammary Tissue of Cows. http://www.wzw.tum.de/gene-quantification/immuno.html#papers Insulin-like growth factor and insulin receptors in intestinal mucosa of neonatal calves. http://www.wzw.tum.de/gene-quantification/endo.html#igfs Determination of real-time PCR efficiency (also in competitive RT-PCR) http://www.wzw.tum.de/gene-quantification/efficiency.html NEW EQUATIONS & ALGORITHM by Tichopad et al. 2002 http://www.wzw.tum.de/gene-quantification/efficiency.html#e-fluoro-sig-2 NEW MOVIES http://www.wzw.tum.de/gene-quantification/movie.html e.g. Molecular Biology, PCR, RPA, Electrophoresis, Northern- & Southern-Blot NEW PUBLICATIONS about kinetic PCR http://www.wzw.tum.de/gene-quantification/real-time.html and http://www.wzw.tum.de/gene-quantification/literature.html Poster boards (a little bit slow !!!): http://www.wzw.tum.de/gene-quantification/poster-a.html methodological poster board A: Array verification physiological poster board B: IGFs - Early Response Genes physiological poster board C: Steroid receptors physiological poster board D: Zinc metabolism physiological poster board E: Immunological relevant factors New links & databases: http://www.wzw.tum.de/gene-quantification/link.html http://www.realtimeprimerdatabase.ht.st http://www.realtimeprimers.org/ http://www.pcrlinks.com http://www.pcrlinks.com/variants/real-time_pcr.htm http://www.cyclertest.com/ The COMPLETE Alkami Quick GuideTM for PCR is a (158 pages) http://www.wzw.tum.de/gene-quantification/quick-guide-pcr.pdf EUROGENTEC PCR manual (48 pages) http://www.wzw.tum.de/gene-quantification/eurogentec-qq-booklet.pdf LightCycler University (LCU) http://www.wzw.tum.de/gene-quantification/real-time.html#lcu Please send the NEWSLETTER and the home page links to further scientists and friends who are interested in real-time PCR, new quantification strategies, relative or absolute gene quantification using kinetic PCR. best regards Michael Pfaffl ############################################# For further QUESTIONS concerning real-time PCR and if you want to SUBSCRIBE to our monthly appearing GENE QUANTIFICATION NEWSLETTER please contact gene.quantification@wzw.tum.de You will receive all NEW FEATURES and future REST & REST-XL updates. GENE QUANTIFICATION web page and the GENE QUANTIFICATION NEWSLETTER are non-commercial, educational sites with the only purpose of facilitating access to biology-related information over the internet. The web page is optimised for Netscape Navigator version 4.7 & Internet Explorer version 5.0 (and higher versions) with an optimal screen resolution of 1024 x 768 pixels. GENE QUANTIFICATION web page visits and DOWNLOAD statistics are listed here: http://www.wzw.tum.de/gene-quantification/contact.html#server If you want UN-SUBSCRIBE from all future NEWSLETTERS please contact gene.quantification@wzw.tum.de and type REMOVE into the subject line. You will be removed instantly from our mailing list. ******************************************************************** Gene Quantification @ wzw.tum.de e-mail: gene.quantification@wzw.tum.de homepage: http://www.wzw.tum.de/gene-quantification/index.shtml homepage: http://www.wzw.tum.de/gene-quantification/physiology.shtml responsible Senior Scientist: Dr. Michael W. Pfaffl Institute of Physiology Life Science Center Weihenstephan, Technical University of Munich Weihenstephaner Berg 3 D-85350 Freising-Weihenstephan GERMANY ******************************************************************** --=====================_7570171==_.ALT Content-Type: text/html; charset="us-ascii" Gene Quantification Newsletter - January 2003

Happy New Year 2003
to all Newsletter Readers and Gene Quantification Visitors

NEW features:

RNA and Gene Expression - NEW PUBLICATIONS

Tissue-specific expression pattern of bovine prion gene (PrP): Quantification using real-time RT-PCR
http://www.wzw.tum.de/gene-quantification/absolute.html#prp

Detection and quantification of mRNA-expression of alpha- and beta-adrenergic
receptor subtypes in the mammary gland of dairy cows.
http://www.wzw.tum.de/gene-quantification/endo.html#adrenerg

Gene Quantification in Endocrinology - NEW PUBLICATIONS
Gene Expression of Immunologically Important Factors in Blood Cells, Milk Cells and Mammary Tissue of Cows.
http://www.wzw.tum.de/gene-quantification/immuno.html#papers

Insulin-like growth factor and insulin receptors in intestinal mucosa of neonatal calves.
http://www.wzw.tum.de/gene-quantification/endo.html#igfs

Determination of real-time PCR efficiency
(also in competitive RT-PCR)
http://www.wzw.tum.de/gene-quantification/efficiency.html

NEW EQUATIONS & ALGORITHM by Tichopad et al. 2002
http://www.wzw.tum.de/gene-quantification/efficiency.html#e-fluoro-sig-2

NEW MOVIES
http://www.wzw.tum.de/gene-quantification/movie.html
e.g. Molecular Biology, PCR, RPA, Electrophoresis, Northern- & Southern-Blot

NEW PUBLICATIONS about kinetic PCR
http://www.wzw.tum.de/gene-quantification/real-time.html
and
http://www.wzw.tum.de/gene-quantification/literature.html

Poster boards (a little bit slow !!!):
http://www.wzw.tum.de/gene-quantification/poster-a.html
methodological poster board A: Array verification
physiological poster board B:     IGFs - Early Response Genes
physiological poster board C:     Steroid receptors
physiological poster board D:     Zinc metabolism
physiological poster board E:     Immunological relevant factors

New links & databases:
http://www.wzw.tum.de/gene-quantification/link.html
http://www.realtimeprimerdatabase.ht.st
http://www.realtimeprimers.org/
http://www.pcrlinks.com
http://www.pcrlinks.com/variants/real-time_pcr.htm
http://www.cyclertest.com/

The COMPLETE Alkami Quick GuideTM for PCR is a (158 pages)
http://www.wzw.tum.de/gene-quantification/quick-guide-pcr.pdf

EUROGENTEC PCR manual (48 pages)
http://www.wzw.tum.de/gene-quantification/eurogentec-qq-booklet.pdf

LightCycler University (LCU)
http://www.wzw.tum.de/gene-quantification/real-time.html#lcu

Please send the NEWSLETTER and the home page links to further scientists and friends who are interested in real-time PCR, new quantification strategies, relative or absolute gene quantification using kinetic PCR.

best regards

Michael Pfaffl

#############################################

For further QUESTIONS concerning real-time PCR and if you want to SUBSCRIBE to our monthly appearing GENE QUANTIFICATION NEWSLETTER please contact gene.quantification@wzw.tum.de   You will receive all NEW FEATURES and future REST & REST-XL updates.

GENE QUANTIFICATION web page and the GENE QUANTIFICATION NEWSLETTER are non-commercial, educational sites with the only purpose of facilitating access to biology-related information over the internet. The web page is optimised for Netscape Navigator version 4.7 & Internet Explorer version 5.0 (and higher versions) with an optimal screen resolution of 1024 x 768 pixels.

GENE QUANTIFICATION web page visits and DOWNLOAD statistics are listed here: http://www.wzw.tum.de/gene-quantification/contact.html#server

If you want UN-SUBSCRIBE from all future NEWSLETTERS please contact gene.quantification@wzw.tum.de and type REMOVE into the subject line. You will be removed instantly from our mailing list.

Hi Constantinos,

yes, this is quite easy to do using SRS = ...

an example using the following URL = :

http://iubio.bio.indiana.edu/srs6bin/cgi-bin/wg= etz?-id+7KUJq1KWZKD+-e+[GENBANK:'AB013077']

which returns an azurin sequence entry = from genbank=20 ( you'll probably have to add a final ] to the URL, cut and paste = mressing=20 about). If you scroll down the entry page you will notice that there are = section=20 with CDS, source, gene etc ... if you actually click on the CDS (it is = actually=20 a hyperlink), you get a page containing just that sub-section of = the=20 complete entry. Due to some clever code in SRS, the sequence associated = with=20 this section of the entry is the sequence between the CDS sequence = positions=20 (which I thibk is what you're after). Then it's just a matter of cutting = and=20 pasting that sequence into whatever application or separate file you=20 want.

hope that helps

Benedict Arnold

>Is anyone=20 aware of any software (not commercial), that can be used for =
>extraction=20 of portions of the
>flatfiles ? (I think that's how they call the = GenBank=20 entries you get
>after a search) . For example if in a database = flatfile=20 entry,
>you have a reference to coding sequence as " CDS : 235 = ... 1500=20 bp" , is
>there a software that can find the keyword "CDS" =
>in the=20 flatfile, and then read and return the string composed of the =
>letters a=20 c g t, that is between the numbers 235...1500
>in the sequence at = the end=20 of the file ? I am particularly interested,
>to extract promoter = regions=20 from whole gene entries of
>GenBank.=20

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