Cattle  11.0
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The Gene Indices are built using:

  • megablast [Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14]
  • CAP3, developed by Dr. Xiaoqiu Huang
  • Paracel TranscriptAssembler[tm], from Paracel Inc.
  • DNA-Protein Search program (dps) developed by Dr. Xiaoqiu Huang

The ORF annotation of TCs is done using:

  • ESTScan [ Iseli, C. Jongeneel, C.V., and Bucher, P. (1999) ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.ISMB 7: 138-148. ]
  • DIANA-EST Hatzigeorgiou AG, Fiziev P, Reczko M. Related Articles DIANA-EST: a statistical analysis. Bioinformatics. 2001 Oct;17(10):913-9.
  • framefinder Expressed Sequence Tag Analysis Tools Etc (c) Guy St.C. Slater 1996-1999. Human Genome Mapping Project RC, Hinxton, Cambridge, UK.

The Genome mappings are done using:

  • blest (C) Webb Miller - see reference
  • Scout[tm], from Paracel Inc.
  • gap2 developed by Dr. Xiaoqiu Huang
  • Transcription binding sites references:
    • Marinescu VD, Kohane IS, Riva A. MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics 2005, 6(1):79.
    • Marinescu VD, Kohane IS, Riva A. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res. 2005, 33:D91-7.
    • Matys V, Fricke E, Geffers R, Gößling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Münch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 2003, 31:374-8.
    • Kel AE, Gößling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E. MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 2003, 31:3576-9.

The expression profiles of the ESTs are scored using:

  • 'R' statistic (Stekel, Git, and Falciani (2000) The comparison of gene expression from multiple cDNA libraries. Genome Research 10:2055-2061).

The unique oligomers for the TCs are generated using:

  • OligoPicker (Xiaowei Wang and Brian Seed (2003) Selection of Oligonucleotide Probes for Protein Coding Sequences. Bioinformatics 2003 May 1;19(7):796-802).

Domain annotation of TCs is done using:

  • Reverse Position Specific BLAST Marchler-Bauer A et al. (2003), "CDD: a curated Entrez database of conserved domain alignments", Nucleic Acids Res. 31:383-387.
  • Pre calculated PSSMS for the Pfam and Smart databases have been downloaded from NCBI, while the Psi-blast/makemat/copymat/formatdb suite of utilities has been used to generate the Prodom PSSM database.

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   The Gene Index Project is supported in part by funding from the US National Science Foundation through grant #DBI-0552416.