Journal ArticleDOI
GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes.
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TLDR
GAMOLA was designed to handle the numerous scaffolds and changing contents of draft phase genomes in an automated process and stores the results for each predicted ORF in flatfile databases.Abstract:
Laboratories working with draft phase genomes have specific software needs, such as the unattended processing of hundreds of single scaffolds and subsequent sequence annotation. In addition, it is critical to follow the "movement" and the manual annotation of single open reading frames (ORFs) within the successive sequence updates. Even with finished genomes, regular database updates can lead to significant changes in the annotation of single ORFs. In functional genomics it is important to mine data and identify new genetic targets rapidly and easily. Often there is no need for sophisticated relational databases (RDB) that greatly reduce the system-independent access of the results. Another aspect is the internet dependency of most software packages. If users are working with confidential data, this dependency poses a security issue. GAMOLA was designed to handle the numerous scaffolds and changing contents of draft phase genomes in an automated process and stores the results for each predicted ORF in flatfile databases. In addition, annotation transfers, ORF designation tracking, Blast comparisons, and primer design for whole genome microarrays have been implemented. The software is available under the license of North Carolina State University. A website and a downloadable example are accessible under (http://fsweb2.schaub. ncsu.edu/TRKwebsite/index.htm).read more
Citations
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Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM
Eric Altermann,W. Michael Russell,M. Andrea Azcarate-Peril,Rodolphe Barrangou,B. Logan Buck,Olivia McAuliffe,Olivia McAuliffe,Nicole Souther,Alleson Dobson,Tri Duong,Michael Callanan,Michael Callanan,Sonja Lick,Sonja Lick,Alice Hamrick,Raul J. Cano,Todd R. Klaenhammer +16 more
TL;DR: L. acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972 and the complete genome is 1,993,564 nt and devoid of plasmids as mentioned in this paper.
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The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533
R. David Pridmore,Bernard Berger,Frank Desiere,David Vilanova,Caroline Barretto,Anne Cecile Pittet,Marie Camille Zwahlen,Martine Rouvet,Eric Altermann,Rodolphe Barrangou,Beat Mollet,Annick Mercenier,Todd R. Klaenhammer,Fabrizio Arigoni,Mark A. Schell,Mark A. Schell +15 more
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References
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