Sequencing Bacillus anthracis Typing Phages Gamma and Cherry Reveals a Common Ancestry

The genetic relatedness of the Bacillus anthracis typing phages Gamma and Cherry was determined by nucleotide sequencing and comparative analysis. The genomes of these two phages were identical except at three variable loci, which showed heterogeneity within individual lysates and among Cherry, Wβ, Fah, and four Gamma bacteriophage sequences

Mouse BAC Ends Quality Assessment and Sequence Analyses

A large-scale BAC end-sequencing project at The Institute for Genomic Research (TIGR) has generated one of the most extensive sets of sequence markers for the mouse genome to date. With a sequencing success rate of >80%, an average read length of 485 bp, and ABI3700 capillary sequencers, we have generated 449,234 nonredundant mouse BAC end sequences (mBESs) with 218 Mb total from 257,318 clones from libraries RPCI-23 and RPCI-24, representing 15× clone coverage, 7% sequence coverage, and a marker every 7 kb across the genome. A total of 191,916 BACs have sequences from both ends providing 12× genome coverage. The average Q20 length is 406 bp and 84% of the bases have phred quality scores ≥ 20. RPCI-24 mBESs have more Q20 bases and longer reads on average than RPCI-23 sequences. ABI3700 sequencers and the sample tracking system ensure that > 95% of mBESs are associated with the right clone identifiers. We have found that a significant fraction of mBESs contains L1 repeats and ∼48% of the clones have both ends with ≥ 100 bp contiguous unique Q20 bases. About 3% mBESs match ESTs and > 70% of matches were conserved between the mouse and the human or the rat. Approximately 0.1% mBESs contain STSs. About 0.2% mBESs match human finished sequences and > 70% of these sequences have EST hits. The analyses indicate that our high-quality mouse BAC end sequences will be a valuable resource to the community

Linear Representations of Prophage Regions

<p>Regions are (from top to bottom): CMLP1, CJIE2, CJIE4, CLIE1, and CUIE1. Colors of ORFs are indicated in the key by putative phage function. Connecting lines represent those ORFs whose protein sequences match at a BLASTP of 30% identity or better. These lines do not indicate the coordinates of match, merely that there is a match.</p

Phylogenetic Analysis and Frequency Distribution of Protein Percent Identity

<p>Concensus maximum-likelihood trees are depicted using multiple alignments of 16S rRNA (A) or 12 concatenated protein datasets (B). The numbers along the branches denote percent occurrence of nodes among 100 bootstrap replicates. The scale bar represents the number of nucleotide (A) or amino acid (B) substitutions.</p

Whole-Genome Comparison of Five <i>Campylobacter</i> Strains

<p>Line figures depict the results of PROmer analysis. Colored lines denote percent identity of protein translations and are plotted according to the location in the reference (C. jejuni RM1221, x-axis) and query genomes (C. jejuni NCTC 11168 [upper y-axis] and C. coli RM2228 [lower y-axis]) (A). The Venn diagrams show the number of proteins shared (black) or unique (red) within a particular relationship for all five <i>Campylobacter</i> strains (B) and for members of the sequenced ε-Proteobacteria compared in this study (C). Protein sequences binned as “unique” are unique within the context of the genomes plotted and the cutoffs used to parse the BLASTP data. The pie charts plot the number of protein sequences by main functional role categories for C. jejuni RM1221 ORFs. A frequency distribution of protein percent identity (D) was computed: specifically, the number of protein sequences within class intervals of 5% amino acid identity from 35% to 100% that match C. jejuni RM1221 reference sequences were plotted.</p