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, Rland 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.

The number of bacterial genomes collected by Genome Information Broker of DDBJ [2] has increased every week and will reach 1000 genomes in September 2009. Thanks to the revolution of the sequencing technology, many microbiologists will get genome sequences of their favorite strains. It is certain that we will soon observe tsunami of genome sequences. However, it is uncertain that every microbiologist is able to fully utilize the genome sequence for their research. The biological knowledge will remain only a drop in the ocean, if the bottleneck is not removed. The bottleneck is the annotation. Therefore, we have developed a microbial genome annotation pipeline (MiGAP) to support for novice and old pro alike to interpret sequences.