References
Use this when refering MiGAP
Sugawara H, Ohyama A, Mori H and Kurokawa K. (2009) "Microbial Genome Annotation Pipeline (MiGAP) for diverse users" The 20th International Conference on Genome Informatics (GIW2009) Poster and Software Demonstrations (Yokohama), S001-1-2
References for ORF Prediction software and databases in the MiGAP Pipeline
ORF Prediction
Noguchi, H., Taniguchi, T. and Itoh, T., MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes, DNA Res. 15(6):387-96, 2008.
A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved microbial gene identification with GLIMMER, Nucleic Acids Research 27:23 (1999), 4636-4641.
RNA Prediction
Lagesen K, Hallin PF, Rland E, St誡feldt HH, Rognes T Ussery DW RNammer: consistent annotation of rRNA genes in genomic sequences Nucleic Acids Res. 2007 Apr 22.
Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res, 25, 955-964.
Homology Search
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.
Tatusov RL, Koonin EV, Lipman DJ. ,Science. 1997 Oct 24;278(5338):631-7. A genomic perspective on protein families.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. , BMC Bioinformatics. 2003 Sep 11;4:41. Epub 2003 Sep 11. The COG database: an updated version includes eukaryotes.