Category Archives: ADVANCES IN

THE THIRD GENERATION SEQUENCER

While the increasing usage and new modification in next generation se­quencing, the third generation sequencing is coming out with new insight in the sequencing. Third-generation sequencing has two main character­istics. First, PCR is not needed before sequencing, which shortens DNA preparation time for sequencing. Second, the signal is captured in real time, which means that the signal, no matter whether […]

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454 GS FLX TITANIUM SOFTWARE

GS RunProcessor is the main part of the GS FLX Titanium system. The software is in charge of picture background normalization, signal location correction, cross-talk correction, signals conversion, and sequencing data generation. GS RunProcessor would produce a series of files including SFF (standard flowgram format) files each time after run. SFF files con­tain the basecalled sequences and corresponding quality scores […]

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NITROGEN LIMITATION AFFECTS THE NITROGEN — ASSIMILATORY PATHWAY AT THE TRANSCRIPTOME LEVEL

We identified a number of genes that encode for components of the ni­trogen assimilatory pathway (Table 4). Genes that encode for enzymes catalyzing the reduction of NO3- to NH4+ and the biosynthesis of nitrogen­carrying amino acids were strongly expressed under nitrogen limitation [32,33]. Along with the pentose phosphate pathway, these genes were among the most up-regulated genes in — N […]

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DISCUSSION OF NGS APPLICATIONS

Fast progress in DNA sequencing technology has made for a substantial reduction in costs and a substantial increase in throughput and accuracy. With more and more organisms being sequenced, a flood of genetic data is inundating the world every day. Progress in genomics has been moving steadily forward due to a revolution in sequencing technology. Addition­ally, other of types-large scale […]

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EXPANDED ANNOTATION COVERAGE

The methods described to compensate for the incomplete annotation cov­erage of Chlamydomonas reinhardtii genes resulted in the addition of a vast number of unique annotations to the genome. While there is a strong overlap between pre-existing annotations and those assigned by inference, many new terms have also been added. The annotations derived by orthology,

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AB SOLID SYSTEM

(Sequencing by Oligo Ligation Detection) SOLiD was purchased by Ap­plied Biosystems in 2006. The sequencer adopts the technology of two — base sequencing based on ligation sequencing. On a SOLiD flowcell, the libraries can be sequenced by 8 base-probe ligation which contains liga­tion site (the first base), cleavage site (the fifth base), and 4 different fluo­rescent dyes (linked to the […]

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STARCH SYNTHESIS UNDER NITROGEN LIMITATIONS

While several genes associated with the preparatory steps in starch synthe­sis are up-regulated in the — N case, the genes encoding for key enzymes AGPase and starch synthase were repressed (Table 1). The degradative side of starch metabolism, specifically a-amylase which hydrolyzes starch to glucose, was also strongly repressed during nitrogen limitations. When coupled to the increased but still overall […]

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ALGAL FUNCTIONAL ANNOTATION TOOL: A WEB-BASED ANALYSIS SUITE TO FUNCTIONALLY INTERPRET LARGE GENE LISTS USING INTEGRATED ANNOTATION AND EXPRESSION DATA

DAVID LOPEZ, DAVID CASERO, SHAWN J. COKUS, SABEEHA S. MERCHANT, and MATTEO PELLEGRINI 11.1 BACKGROUND Next-generation sequencers are revolutionizing our ability to sequence the genomes of new algae efficiently and in a cost effective manner. Several assembly tools have been developed that take short read data and assemble it into large continuous fragments of DNA. Gene prediction tools are also […]

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EXAMPLE: SULFUR-RELATED GENES

Using a filtered list of C. reinhardtii genes derived from transcriptome se­quencing of the green alga under sulfur-depleted conditions [26], the Algal Functional Annotation Tool found enrichment for annotations related to sulfur metabolism, cysteine and methionine metabolism, and sulfur com­pound biosynthesis. For each annotation, the results may be expanded to reveal the genes containing that particular annotation. Furthermore, there is […]

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