J. N. Marchaukoski

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words counted: 159 / limit: 350) Background: Similarity search of a given protein sequence against a database is an essential task in genome analysis. Sequence alignment is the most used method to perform such analysis. Although this approach is efficient, the time required to perform searches against large databases is always a challenge. Alignment-free(More)
Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as(More)
We report the complete genome sequence of Herbaspirillum hiltneri N3 (DSM 17495), a member of the genus Herbaspirillum of the Betaproteobacteria. The genome is contained in a single chromosome, and analysis revealed that N3 lacks the whole nitrogen fixation (nif) gene cluster, confirming its inability to fix nitrogen.
There are several guidelines for gene nomenclature, but they are not always applied to the names of newly identified genes. The lack of standardization in naming genes generates inconsistent databases with errors such as genes with the same function and different names, genes with different functions and the same name, and use of an abbreviated name. This(More)
Herbaspirillum huttiense subsp. putei strain 7-2T (IAM 15032) is a betaproteobacterium isolated from well water in Osaka, Japan. It was first described as a new species, Herbaspirillum putei, closely related to H. huttiense (1). Later, 16S rRNA gene resequencing and DNA-DNA hybridization analysis led to the reclassification of H. putei as a subspecies of H.(More)
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