Splice Junction Analysis Service

sequence walker Jim Ellis (DHHS/NIH/OD/ORS/DBEPS, jrellis@helix.nih.gov, voice: 301-496-4472, fax: 301-480-1242, Bldg. 13, Rm 3E-49, NIH directory entry) has set up Tom Schneider's Delila programs to do splice junction analyses for scientists at NIH (P. K. Rogan, B. M. Faux and T. D. Schneider, Information analysis of human splice site mutations Human Mutation 12(3): 153-171 (1998).) Published or unpublished sequence data can be used but it is most efficient to start with GenBank flat file format. Mutations are expressed in a precise computer language called Delila.

Dr. Ellis also does analyses as collaborations with people outside NIH if he has time.

Dr. Ellis can begin the analysis if he has:

  1. The sequence, in decreasing order of preference as: and
  2. The exact sequence change(s).

Sequences and delila instructions can be given to Jim on a floppy disk or by email.

Tips:

Publications

  1. Splice mutations in NF2, Kluwe Lan, Heinrich B, Ellis JR, Schneider TD, MacCollin M, Mautner V-F. Abstract presented at the 8th European Neurofibromatosis Meeting; September 23-26, 1999; Ulm, Germany.
  2. Molecular Genetics and Metabolism 73 (4), August 2001, 333-339 (doi:10.1006/mgme.2001.3209) Is the SLC7A10 Gene on Chromosome 19 a Candidate Locus for Cystinuria? Daniel Leclerc, Qing Wu, James R. Ellis, Paul Goodyer, Rima Rozen PubMed Abstract
  3. Leclerc, D., M. Boutros, D. Suh, Q. Wu, M. Palacin, J. R. Ellis, P. Goodyer, and R. Rozen. "SLC7A9 mutations in all three cystinuria subtypes", Kidney Int, 62(5): pp. 1550-1559 (2002). PubMed Abstract
  4. Hellerud, C., A. Burlina, C. Gabelli, J. R. Ellis, P.-G. Nyholm, and S. Lindstedt. "Glycerol Metabolism and Determination of Triglycerides - Clinical, Biochemical, and Molecular Findings in Six Subjects". Clinical Chemistry and Laboratory Medicine, Vol. 41 (2003), pp. 46-55. PubMed Abstract
  5. Hellerud, C., M. Adamowicz, D. Jurkiewicz, J. Taybert, J. Kubalska, E. Ciara, E. Popowska, J. R. Ellis, S. Lindstedt and E. Pronicka. "Clinical heterogeneity and molecular findings in five Polish patients with glycerol kinase deficiency: investigation of two splice site mutations with computerized splice junction analysis and Xp21 gene-specific mRNA analysis". Molecular Genetics and Metabolism, 79(3) (2003), pp. 149-159. PubMed Abstract
  6. J. E. Cleaver, C. Collins, J. Ellis and S. Volik, "Genome sequence and splice site analysis of low-fidelity DNA polymerases H and I involved in replication of damaged DNA, Genomics", Volume 82, Issue 5, November 2003, Pages 561-570. PubMed Abstract; at www.sciencedirect.com
  7. Goldin E, Stahl S, Cooney AM, Kaneski CR, Gupta S, Brady RO, Ellis JR, Schiffmann R. Transfer of a mitochondrial DNA fragment to MCOLN1 causes an inherited case of mucolipidosis IV. Hum Mutat. 2004 Dec;24(6):460-5. PubMed Abstract.
  8. Genes Chromosomes Cancer. 2011 Aug;50(8):571-84. Effects of splicing mutations on NF2-transcripts: Transcript analysis and information theoretic predictions. Ellis JR Jr, Heinrich B, Mautner VF, Kluwe L. PubMed Abstract.

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Schneider Lab

origin: 1999 Apr 30
updated: 2011 Jun 27
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