Journal: BMC Bioinformatics

Article Title: A novel approach to sequence validating protein expression clones with automated decision making

doi: 10.1186/1471-2105-8-198

Figure Lengend Snippet: Illustration of Gap Mapper algorithm for contig calculation . Clone reads deemed to be of sufficient quality are supplemented by a pseudo read generated from the reference sequence with all bases set to a confidence score of 19 and submitted to the Phrap assembly process. The alignment matrix of clone reads is retrieved from Phrap output in order to determine the positions of each read relative to the reference sequence. Consensus sequences and confidence scores are computed for the various contigs using a naïve Bayes classifier, and the results are reported. The calculated contigs are trimmed to drop low confidence tails.

Article Snippet: Some basic sequencing programs handle pre-processing of sequence trace files, base calling [ ], quality clipping, vector trimming and removal [ ], contig assembly (phrap [ ] or TIGR assembler [ ]) and primer design [ ].

Techniques: Generated, Sequencing

Journal: PLoS ONE

Article Title: Persistent Infection and Promiscuous Recombination of Multiple Genotypes of an RNA Virus within a Single Host Generate Extensive Diversity

doi: 10.1371/journal.pone.0000917

Figure Lengend Snippet: Unrooted, consensus phylogenetic trees were obtained from 2,000,000 generations of the Markov chain Monte Carlo simulation in Bayesian analysis using a general time-reversal model of nucleotide substitution . The number above each branch indicates the Bayesian posterior probability. The scale bars represent 0.1 expected substitutions per site. Branch lengths are proportional to evolutionary distance. Sequences were aligned using ClustalX and subsequently manually aligned prior to the Bayesian phylogenetic analysis. A, Known CTV genomes and CTV genomes assembled from resequencing analysis of FS2-2 (highlighted orange). The suffix at the end of fs2_2 distinguishes multiple genotypes in the isolate and also indicates the anchor sequence from which the consensus contig was generated by the Phrap program. B, the 5′ proximal 1 kb, and C, p33-coding region of CTV genomes obtained by direct sequencing of RT-PCR clones. In both B and C, Bayesian posterior probability and clones with identical sequences were omitted for clarity. Recombinant sequences are highlighted in green.

Article Snippet: These fragments and the quality scores associated with each base call were used in contig assembly by the Phrap program as implemented in the CodonCode Aligner program.

Techniques: Sequencing, Generated, Reverse Transcription Polymerase Chain Reaction, Clone Assay, Recombinant