Chenna Ramu, European Molecular Biological Laboratory, Heidelberg, Germany

@ About ...

I am from India. My old home-page
Contact:
Chenna Ramu
European Molecular Biological Laboratory
1, Meyerhofstrasse, 69117, Heidelberg, Germany.
Ph: 49-6221-387530, Fax: 49-6221-387517

email: chenna at embl dot de

@ College/University

• Ph.D (Heidelbreg University)
• Post Graduation in Mathematics (M.Sc, 2 year)
• Under Graduation in Mathematics (B.Sc, 3 year) [First in College]

@ Embl

I started my EMBL career with Thure Etzold working for the famous Sequence Retrieval System (SRS). I am one of the four other SRS team members. It was a great project! Google is the keyword for web search. SRS is the keyword for data integration in biology.
• I have been working with Toby Gibson. I am involved in system administration of Unix/Linux systems in our group and setting and maintining servers. We have set up a number of servers for internal and external researchers.
  • Bioccelerator
  • Gene2Est
  • RepeatMasker
  • SIRW [You could search for your protein motif ...]
  • Protein Motif Pattern Maker
  • Protein Motif Mapper [ you could use this server for DNA/RNA too... ]
  • SRS
  • BLAST2SRS
  • ELM, ...
  • There is a alternative splice site predictor I developed few years back. The 'staden package' use our data set.
• I have ported Clustalx for Mac OS X. Fetch it from ClustalX and Clustalw for Mac X
• Recently we made Sun solaris 32 and 64 bit versions of ClustalX and Clustalw
• I have developed a smith-waterman search system (yet to be published).
• My interest lies in developing algorithm to solve biological problems. I have been working on improving ClustalW/ClustalX. There is enough knowledge now to replace some of the heuristics in clustal. We are trying to do this in a number of ways, for example developing new series amino acid exchange matrices [bin matrices], bringing in more realistic gap functions and reducing the number of parameters for multiple alignment problem [If you have four parameter that is good enough number to fit an elephant]

@ Leisure

I do play games. Table Tennis, Badminton, Basketball, ...
Football (Soccer) is my favourite. For creativity Argentina, domination and elegance Brazil, for power and speed most of the european coutries. Somehow for Asian countries world-cup is too late! I want one of the African country to win this time! Come on Africa!
World-Cup 2006
Reading books, (Complex solution for a simple problem read Fermat's Last Theorem by Simon Singh) and
Comics, most of pocket money went to this british agent Irumbukkai Maayavi

@ Publications

• Multiple sequence alignment with the Clustal series of programs. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD.
  Nucleic Acids Res. 2003 Jul 1;31(13):3497-500.
• SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches. Ramu C.
  Nucleic Acids Res. 2003 Jul 1;31(13):3771-4.
• ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
  Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferre F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Kuster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ.
  Nucleic Acids Res. 2003 Jul 1;31(13):3625-30.
• SIR: Simple Indexing and Retrieval System for biological databases
  Chenna Ramu
  Bioinformatics 2001 17: 756-758.
• Gene2EST - a BLAST server for searching Expressed Sequence TAG (EST) databases with eukaryotic gene-sized queries.
  Christine Gemuend, Chenna Ramu, Brigitte-Altenberg-Gruelich and Toby J. Gibson
  Nucleic Acids Res 2001 Mar 15;29(6):1272-1277
• Object-oriented parsing of biological databases with Python
  Chenna Ramu, Christine Gemuend and Toby J. Gibson
  Bioinformatics, Volume 16, Issue 7, Pages 628-638 : July 2000
• cgimodel: CGI Programming Made Easy with Python
  Chenna Ramu et al.,
  Linux Journal #75, July, Pages 142-149, 2000
• The APECED Polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor.
  Toby J. Gibson, Chenna Ramu, Christine Gemuend and Rein Aasland
  TIBS, July 1998, (242-244).
• Generating Dynamic Documents From Templates
  Chenna Ramu Digital Systems Report, Summer, 1998, Page(14-19)
• Methanog: a specialized database on Methenogenic bacteria.
  Thakur AR, Ramu C, Parrack PK,Mukhopadhyay S
  Protein Sequence Data Analysis 1991, 4(6):363-6