About the Website for the T4-like Phages

Unique Resources

Phage-specific BLAST server

Users can perform NCBI BLAST sequence searches against bacteriophage genomes. This feature allows rapid searching of a focused set of genomes and databases. Available genomes include T4, RB69, RB49 and the Aeromonas hydrophila phage, Aeh1, plus contig assemblies from coliphage RB43. E. coli genome and Swiss Protein database searches are available on a limited basis.

Phage Genome Browsers

Interactive browsing of completed phage genomes is available using Lincoln Stein's Generic Genome Browser program. The browser allows users to scan the genome for particular features and to download sequence information plus analyses of those features. Views of the genome are generated showing named genes, BLAST similarities to other phages, predicted tRNAs, terminators and introns. Links are provided from the browser to gene-specific pages, with DNA sequence, protein sequence, protein statistics, sequence alignment to T4 orthologs, hydropathy plots and Pfam protein domain matches.

Phage Forum

This Message Board allows informal discussion for the T4 community. Users are encouraged to provide comments and observations about their own research as well as this site.

Other Phage Information

Pages with links to phage information are also available, including a T4 genetic map reference figure, RB69, RB49, and Aeh1 Map figures, electron micrographs, annotation tables, sequence files, and links to NCBI T4 and Integrated Genomics RB69 annotation sites are available. Links to other web pages with information about T4-like bacteriophage are also listed.

	Supported by a grant from the National Science Foundation: Microbial Genome Sequencing: Sequencing Genomes of the Myoviridae.
	Tulane University, New Orleans, LA [Jim Karam, Ph.D., Vasiliy Petrov Ph.D., James Nolan, Ph.D., Dawn Chin] CNRS, Toulouse, France [Henry Krisch, Ph.D., Andrej Letarov, Ph.D., Claire Bertrand, Ph.D., Stefanie Müller]

Genome Browser Information

Phage Genome browser information

The genome browser can be configured by the user to show desired information from the available options. Full instructions are available for the various browser functions on the Browser Help Page, in addition to this summary. Information tracks may be added or removed by clicking the check boxes next to the track name. Clicking the track name links to a help page with descriptions of each track (also shown below). The view can be updated by clicking the "Update Image" button. The length of genome viewed can be adjusted by selecting the desired length from the menu bar at the top of the display. The region of the genome viewed can be selected by clicking on the tan overview scale at the top of the viewer, or scrolled using arrows flanking the size menu bar. Particular genes or gene products may be accessed directly by entering the name in the "Landmark" box and clicking "Go". Very limited searching is possible, but some near-matches may not give the desired gene. Clicking on particular tracks in the browser will produce differing results, depending upon the track. For example, clicking on a gene arrow will link to a page describing the gene product. Clicking on a BLAST hit will link to a browser view of the similar gene in the corresponding phage genome. Descriptions of links for other tracks are included in the detailed information for each track.

T4 Browser: Available Tracks

Named Genes Named genes from the Genbank Bacteriophage T4 Genome as updated by Eric Miller (Miller, E.S., E. Kutter, G. Mosig, F. Arisaka, T. Kunisawa and W. Rüger. 2003. Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 67:86 - 156). Note that ORFs of unknown function are named in T4. Genes are linked to individual pages with FASTA format DNA of the coding region, protein sequence, EMBOSS pepstats protein statistics, (mol. weight, pI, composition), Clustal multiple sequence alignment to presumed orthologs in T4-related phages, EMBOSS octanol hydropathy plot, link to GenBank page for each gene, and Pfam protein domain function matches. Coding sequence Exon boundaries of coding region for genes that contain non-translated segments (e.g. intron-containing genes and frameshfted genes. Not an indication of boundaries of 5' and 3' ends of transcribed (polycistronic) mRNA. tRNAs Predicted tRNAs using Sean Eddy's tRNAscan-SE program. Predicted acceptor amino acid is listed. Other possible amino acids based on similarity to known tRNAs also given. RB69-BLAST Hits BLASTx hits (E<0.001) of translated T4 DNA to protein sequences of the Bacteriophage RB69 Genome. RB49-BLAST Hits BLASTx hits (E<0.001) of translated T4 DNA to protein sequences of the Bacteriophage RB49 Genome. Aeh1-BLAST Hits BLASTx hits (E<0.001) of translated T4 DNA to protein sequences of the Bacteriophage Aeh1 Genome. DNA Percent GC plot for windows of genomic sequence. Noncoding RNAs Non-coding RNA regions, such as group I introns. 3-frame translation (forward) Shows predicted amino acids for all 3 forward open reading frames at high magnifications. Shows only sites of predicted stop codons in lower resolution views. 3-frame translation (reverse) Shows predicted amino acids for all 3 reverse open reading frames at high magnifications. Shows only sites of predicted stop codons in lower resolution views. GeneMark GeneMarkS predicted open reading frames. glimmer Predicted ORFs using glimmer2.02 Curated promoter/terminator Curated promoter and terminator sequences. From Betty Kutter'sT4orfs.XLS file. Length of region arbitrarily set to 100 bp downstream of promoter or 100 bp upstream of terminator for visual clarity. Terminator Predicted rho-independent terminators using the TIGR TransTerm program. Length of stem in base pairs is indicated.

RB69, RB49, Aeh1Browser: Available Tracks

Named gene Gene predictions based upon homology of ORFs to the Bacteriophage T4 Genome or to related phages. Genes are linked to individual pages with FASTA format DNA of the coding region, protein sequence, EMBOSS pepstats protein statistics, (mol. weight, pI, composition), EMBOSS Smith-Waterman optimal alignment to presumed T4 ortholog, EMBOSS octanol hydropathy plot, and Pfam protein domain function matches. T4-BLASTx Hits BLASTx hits (E<0.001) of translated RB69 DNA to protein sequences of the Bacteriophage T4 Genome. Linked to Gene Browser of corresponding locus on T4 genome browser page. RB69-BLAST Hits BLASTx hits (E<0.001) of translated T4 DNA to protein sequences of the Bacteriophage RB69 Genome. RB49-BLAST Hits BLASTx hits (E<0.001) of translated T4 DNA to protein sequences of the Bacteriophage RB49 Genome. Aeh1-BLAST Hits BLASTx hits (E<0.001) of translated T4 DNA to protein sequences of the Bacteriophage Aeh1 Genome. ORF Open reading frames without significant similarity to Bacteriophage T4 Genome (E<0.001). tRNAs Predicted tRNAs using the tRNAscan-SE program. Predicted acceptor amino acid is listed. Other possible amino acids based on similarity to known tRNAs also given. BLASTX Hits BLASTx hits (E<0.001) of translated RB69 DNA to the Swissprot protein or GenBank non-redundant database. Linked to GenBank file of the BLAST hit. Only hits for regions not similar to T4 are shown. DNA Percent GC plot of windows of genomic sequence. T4 Insertion Sites of genes present in T4 with known function, but missing in RB69. Named T4 ORFs of unknown function are not noted if missing in RB69. 3-frame translation (forward) Shows predicted amino acids for all 3 forward open reading frames at high magnifications. Shows only sites of predicted stop codons in lower resolution views. 3-frame translation (reverse) Shows predicted amino acids for all 3 reverse open reading frames at high magnifications. Shows only sites of predicted stop codons in lower resolution views. GeneMark GeneMarkS predicted open reading frames. glimmer Predicted ORFs using glimmer2.02 Terminator Predicted rho-independent terminators using the TIGR TransTerm program. Length of stem in base pairs is indicated.