From Kasymir at gmx.net Tue Aug 23 12:50:17 2005 From: Kasymir at gmx.net (Steffen Fehrmann) Date: Tue Aug 23 16:17:37 2005 Subject: [Bio-srs] Question about amino acid substitution matrices Message-ID: <1124819416.983529.78280@g14g2000cwa.googlegroups.com> Hi, I'm a student of biology and one of my main focuses is bioinformatics. At the moment I'm preparing for my final exam. I read about that there are different bit units in different amino acid substitution matrices, e.g. the BLOSUM62 Matrix, which is scaled in 1/2 bit units or the PAM 250, in 1/3 bits (Bioinformatics, Mount, D.W.). I wouldn't care but gap penalty scores depend on these scales. Despite I read how these matrices are generated, I didn't find a description about the differences between 1/2 and 1/3 scaled aa substitution matrices. So, what does that mean and how do the matrices discriminate? I hope anyone could help me and thank you for trying, Steffen From volker.weinberger at novartis.com Wed Aug 24 03:16:11 2005 From: volker.weinberger at novartis.com (volker.weinberger@novartis.com) Date: Wed Aug 24 08:41:40 2005 Subject: [Bio-srs] Question about amino acid substitution matrices Message-ID: Dear Steffen, in fact there are even different versions of BLOSUM62, both for 1/3 bit scaling and 1/2 bit scaling. Gap penalties need to be adjusted to scaling. Discussion on the impact of different scaling on optimal gap penalties can e.g. be found in: - J.T. Reese, W. R. Pearson: Bioinformatics (2002), 18:1500-1507, http://www.people.virginia.edu/~wrp/papers/bioinfo_wrp02jr.pdf - W. R. Pearson: Profein Science (1995), 4:1145-1160 , http://www.proteinscience.org/cgi/reprint/4/6/1145 . Best regards, Volker "Steffen Fehrmann" Sent by: bio-srs-bounces@oat.bio.indiana.edu 23.08.2005 19:50 To: bionet-software-srs@moderators.isc.org cc: (bcc: Volker Weinberger/PH/Novartis) Subject: [Bio-srs] Question about amino acid substitution matrices Category: Hi, I'm a student of biology and one of my main focuses is bioinformatics. At the moment I'm preparing for my final exam. I read about that there are different bit units in different amino acid substitution matrices, e.g. the BLOSUM62 Matrix, which is scaled in 1/2 bit units or the PAM 250, in 1/3 bits (Bioinformatics, Mount, D.W.). I wouldn't care but gap penalty scores depend on these scales. Despite I read how these matrices are generated, I didn't find a description about the differences between 1/2 and 1/3 scaled aa substitution matrices. So, what does that mean and how do the matrices discriminate? I hope anyone could help me and thank you for trying, Steffen _______________________________________________ Bio-srs mailing list Bio-srs@net.bio.net http://www.bio.net/biomail/listinfo/bio-srs From paolo at ist.unige.it Wed Aug 24 04:20:00 2005 From: paolo at ist.unige.it (Paolo Romano) Date: Wed Aug 24 08:41:43 2005 Subject: [Bio-srs] NETTAB 2005 - Deadlines approaching and Staines' talk on Web services-based access to SRS Message-ID: <200508240920.j7O9K0dj011248@ibm43p.biotech.ist.unige.it> Dear all, this is a reminder for next deadlines of the NETTAB 2005 Workshop on "Workflows management: new abilities for the biological information overflow" that will be held on next October 5-7, 2005, in Naples, Italy. The Scientific Programme is now available on-line at http://www.nettab.org/2005/progr.html . The Opening Lecture will be given by Francis Ouellette. Francis Ouellette is the Director of the UBiC, the Bioinformatics Centre of the University of British Columbia, Canada. He is Associate Professor of the Michael Smith Laboratories and of the Department of Medical Genetics of UBC. He is also a core faculty member in the new UBC graduate Training Program in Bioinformatics for Health Research, associate director of Bioinformatics at Genome British Columbia and director of the Canadian Genetic Diseases Network (CGDN) bioinformatics core facility where he helps coordinate the Canadian Bioinformatics Workshops. Francis has an exceptional curriculum and his recent research, training and coordination activities make him one of the most known and appreciated bioinformaticians. The title of his opening talk will be "Workflow management in bioinformatics: the possibilities and the challenges". I would also inform you that daniel Staines from Lion Biosciences will give a purely technical lecture on "Web services-based access to SRS". ---------------------------------------------------------------------- The Call for posters and position papers is closing on next friday August 26, 2005. You are all warmly invited to present your recent activity related to the workshops' topics by submitting a poster abstract (1-2 A4 pages, font size 12 pt, MS Word format) by email to posters2005@nettab.org . Topics are the following: Technologies and technological platforms of interest, with emphasis on: - Web Services (SOAP, WSDL, WSFL, UDDI, ....) - Web Services Choreography and Orchestration - Semantic Web (RDF, LSID, OWL, ...) - comparison of available technologies, limitations, pros and cons - knowledge representation - biological data and knowledge modeling tools - Ontologies, Databases and Applications of Semantics in Bioinformatics Workflow management systems in bioinformatics - implementations of web services - implementations of registries - reuse and versioning of web services and workflows - workflow management systems - web interfaces for accessing and executing workflows - interactive systems to support work flows Applications of workflow management systems in bioinformatics - Methodologies for life sciences analysis, such as: - gene expression, - genome annotation, - mass spec peptide fragment identification, - Encoding of the above in workflows - Case studies - Scenarios and use cases Check all details at: http://www.nettab.org/2005/call.html . -------------------------------------------------------------------------------- The early registration deadline is also next Friday August 26, 2005. The registration form is available on-line at: http://www.nettab.org/2005/rform.html . The payment of the fee can either be done on-line, through the Online Payment Form of the Bioinformatics Italian Society (BITS), or by direct money transfer. Participation fees are as follows: Until August 26, 2005: - Students: 70,00 Euro - Academic: 130,00 Euro (reduced fee: 117,00 Euro) - Non-academic: 270,00 Euro (reduced fee: 243,00 Euro) After August 26, 2005: - Students: 70,00 Euro - Academic: 180,00 Euro (reduced fee: 162,00 Euro) - Non-academic: 370,00 Euro (reduced fee: 333,00 Euro) The 10% reduction on fees is applied for members of: - ISCB (International Society for Computational Biology), http://www.iscb.org/ - BITS (Bioinformatics Italian Society), http://www.bioinformatics.it/ - Hormone Responsive Breast Cancer (HRBC) Genomics Network, http://www.hrbc-genomics.net/ - Oncology over Internet (O2I) project, http://www.o2i.it/ - Interdisciplinary Laboratory for Technologies in Bioinformatics (LITBIO) -------------------------------------------------------------------------------- I'm looking forward to meeting many of you in Naples quite soon. Ciao. Paolo -- Paolo Romano (paolo.romano@istge.it) Bioinformatics and Structural Proteomics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 Web: http://www.nettab.org/promano/