Amino acid (aa) sequence segments similar to those of these three cell-division gene products were searched for from PIR Database, by Lipman-Pearson method using Genentyx Software (Software Development Co., Tokyo). Thus found possibly homologous sequence segments were re-analyzed by dot-matrix method (Harr-Plot), and the corresponding base-sequence alignments (m-base-match in n-base-alignment) ...

An agar-degrading marine bacterium identified as a Microscilla species was isolated from coastal California marine sediment. This organism harbored a single 101-kb circular DNA plasmid designated pSD15. The complete nucleotide sequence of pSD15 was obtained, and sequence analysis indicated a number of genes putatively encoding a variety of enzymes involved in polysaccharide utilization. The mos...

UNLABELLED compcodeR is an R package for benchmarking of differential expression analysis methods, in particular, methods developed for analyzing RNA-seq data. The package provides functionality for simulating realistic RNA-seq count datasets, an interface to several of the most commonly used differential expression analysis methods and extensive functionality for evaluating and comparing diffe...

An algorithm has been developed for the determination of nucleotide sequence from data produced in fluorescence-based automated DNA sequencing instruments employing the four-color strategy. This algorithm takes advantage of object oriented programming techniques for modularity and extensibility. The algorithm is adaptive in that data sets from a wide variety of instruments and sequencing condit...

We have developed a modified BOOTSCAN algorithm that may be used to screen nucleotide sequence alignments for evidence of recombination without prior identification of nonrecombinant reference sequences. The algorithm is fast and includes a Bonferroni corrected statistical test of recombination to circumvent the multiple testing problems encountered when using the BOOTSCAN method to explore ali...

A common challenge in analysis of transcriptomic data is to identify differentially expressed genes, i.e., genes whose mean transcript abundance levels differ across the levels of a factor of scientific interest. Transcript abundance levels can be measured simultaneously for thousands of genes in multiple biological samples using RNA sequencing (RNA-seq) technology. Part of the variation in RNA...

We introduce new techniques to derive compact descriptions of Golay sequences and their extensions. In particular we show how a fundamental notion of commu-tative algebra, namely the notion of Grr obner bases, can be successfully employed to give compact description of Golay sequences. We then concentrate on the practically important case of Golay sequences of length 2 n. For those sequences we...

We have determined the nucleotide sequence of a flagellin gene locus from the haloalkaliphilic archaeon Natrialba magadii, identified the gene products among proteins forming flagella, and demonstrated cotranscription of the genes. Based on the sequence analysis we suggest that different regions of the genes might have distinct evolutionary histories including possible genetic exchange with bac...

Nucleotide sequences of RNA codons have been investigated recently by directing the binding of C'4-AA-sRNA to ribosomes with trinucleotides of defined base sequence. The template activities of 19 trinucleotidest have been described and nucleotide sequences have been suggested for RNA codons corresponding to 10 amino acids.'-5 In this report, the template activities of 26 additional trinucleotid...

A central goal of RNA sequencing (RNA-seq) experiments is to detect differentially expressed genes. In the ubiquitous negative binomial model for RNA-seq data, each gene is given a dispersion parameter, and correctly estimating these dispersion parameters is vital to detecting differential expression. Since the dispersions control the variances of the gene counts, underestimation may lead to fa...