transition from vegetative to reproductive growth is an important stage in plant’s life. flowering pathways including photoperiod, vernalization, gibberellins, and autonomous pathway are regulated by different genes. identification of flowering genes is essential for the development of bolting-resistant sugar beet cultivars. in this study, a set of 118 arabidopsis thaliana genes involved in flo...

Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pairwise fragment overlap. While shotgun sequencing infers a DNA sequence given ...

Sequencing errors and biases in metagenomic datasets affect coverage-based assemblies and are often ignored during analysis. Here, we analyze read connectivity in metagenomes and identify the presence of problematic and likely a-biological connectivity within metagenome assembly graphs. Specifically, we identify highly connected sequences which join a large proportion of reads within each real ...

Next-generation sequencing (NGS) technologies have generated enormous amounts of shotgun read data, and assembly of the reads can be challenging, especially for organisms without template sequences. We study the power of genome comparison based on shotgun read data without assembly using three alignment-free sequence comparison statistics, D(2), D(*)(2) and D(s)(2), both theoretically and by si...

We developed a highly scalable 'shotgun' DNA synthesis technology by utilizing microchip oligonucleotides, shotgun assembly and next-generation sequencing technology. A pool of microchip oligonucleotides targeting a penicillin biosynthetic gene cluster were assembled into numerous random fragments, and tagged with 20 bp degenerate barcode primer pairs. An optimal set of error-free fragments wer...

Weighted sequences are used as profiles for protein families, in the representation of binding sites, and sequences produced by a DNA shotgun sequencing assembly. In this paper we present two simple heuristics for the pattern matching on weighted sequences. One is a simple heuristic which enables a faster validation between a weighted candidate and a weighted text. The other is applying the bad...

While advances in tandem mass spectrometry (MS/MS) steadily increase the rate of generation of MS/MS spectra, standard algorithmic approaches for peptide identification recently seemed to be reaching the limit on the amount of information that could be extracted from MS/MS spectra. However, a closer look reveals that a common limiting procedure is to analyze each spectrum in isolation, even tho...

BACKGROUND Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. ...

UNLABELLED The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum ...