the short-sequence libraries. This was especially pronounced for a Chesapeake Bay virioplankton metagenome library. Increasing the short-read sampling depth or the length of derived short reads (up to 400 bp) did not completely resolve the discrepancy in BLASTX homolog detection. Only in cases where

Sanger-like read lengths- the power of next-gen throughput Uncover more of your genome, transcriptome or metagenome of interest with extended Sanger-like read lengths from the GS FLX+ System. Improvements in sequencing chemistry, instrumentation and software offer the latest in GS FLX System

conservation in regulatory regions and with generation of full-length open reading frames. Patterns of AS and APA were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3

level for each article being read (1-5), and then learning a user profile based on these ratings. This paper describes how NewsWeeder accomplishes this task, and examines the alternative learning methods used. The results show that a learning algorithm based on the Minimum Description Length (MDL

splice site consenses, codon bias, exon/intron length preferences, and open reading frame analysis all in one scoring system. How should all those parameters be set? How should different kinds of information be weighted? A second issue is being able to interpret results probabilistically. Finding a best

Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of length, GapLength) opens a possibility to transform short mate-pairs into long mate-reads of length

clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencing coverage, read length, and error rate. For fixed costs, short Illumina reads can be generated at higher coverage and allow for detecting variants at lower frequencies. They can also

Efficient alignment algorithms are needed to keep up with the continued growth in sequencing tech-nologies. While Smith-Waterman-based methods continue to improve, many practitioners still prefer faster heuristic methods despite the lack of a guarantee in optimality. Seed-and-extend heuristics (as used by BLAST) employ fixed-size seeds (or words) as starting points for local alignment.

Transcriptome assembly using RNA-seq data- particularly in non-model organisms has been dramatically improved, but only recently have the pre-assembly procedures, such as sequencing depth and error correction, been studied. Increasing read length is viewed as a crucial condition to further improve

in the first 32…64bp, has limitation on the minimum read length (32bp), and no limitation on the maximum read length. The number of references is unlimited with total number of base-pairs limited to 2 32. BRAT-bw currently does not support insertions or deletions. Feature comparison of BRAT-bw and other