T4-like genome database: Difference between revisions
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| width='30%' | Who: | | width='30%' | Who: | ||
| | | Jim Nolan | ||
Tulane Univ. | |||
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| width='30%' | What: | | width='30%' | What: | ||
| | | Genome information about T4-like bacteriophage | ||
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| Where: | | Where: | ||
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| Upcoming events | | Upcoming events | ||
| | | n/a | ||
|- | |- | ||
| Web Services | | Web Services | ||
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=About {{PAGENAME}}= | =About {{PAGENAME}}= | ||
[http://phage.bioc.tulane.edu/ {{PAGENAME}}] is a site with genome browsers for the annotated genomes of a set of T4-like bacteriophage sequenced at Tulane and elsewhere. | |||
[http://phage.bioc.tulane.edu/ {{PAGENAME}}] is. | |||
=Content= | =Content= | ||
Genome data and [[GBrowse]]-based browsers for T4 family members Bacteriophage RB14, RB32, Acinetobacter phage 133, Aeromonas phage 25, Aeromonas phage 65, Vibrio phage nt-1, bacteriophage phi-1, RB16, RB43, Phage 31, 44RR2.8t, Aeh1, RB49, RB69, T4, P-SSM2, P-SSM4, S-PM2, KVP40. There is also a local BLAST for T4-like phage genomes and a forum for discussion of phage biology and genomics. | |||
=Using {{PAGENAME}}= | =Using {{PAGENAME}}= | ||
==Browsing== | ==Browsing== | ||
The home page lists each of the phage genomes covered and links to their GBrowse pages, a more classic but noninteractive graphical map, FASTA files for proteins, RNAs, and genomes, and links to the NCBI browser and [[Genbank]] pages. Clicking on a gene in the browser brings up a summary page that has much more than the standard GBrowse data page. The data for each gene includes the DNA and protein sequences, statistics about the protein, a popup alignment viewer, and a White-Wimley hydropathy plot. | |||
Tracks in the browser include BLAST hits to the other covered genomes. Clicking on these takes you to the browser for the other phage. | |||
==Searching== | ==Searching== | ||
Searching is via the GBrowse search box | |||
==Usage examples== | ==Usage examples== | ||
=Other sites with related content= | =Other sites with related content= | ||
=Technology= | =Technology= | ||
[[GBrowse]] plus analysis packages used to generate annoation tracks. | |||
==Web Services/API== | ==Web Services/API== | ||
GBrowse includes a Moby interface. Not documented whether it works on this site. | |||
=Discussion= | =Discussion= | ||
| Line 42: | Line 52: | ||
=References= | =References= | ||
=External Links= | =External Links= | ||
[http://phage.bioc.tulane.edu/ {{PAGENAME}}] | [http://phage.bioc.tulane.edu/ {{PAGENAME}}] URL: http://phage.bioc.tulane.edu | ||
==Discussion of {{PAGENAME}} on other websites== | ==Discussion of {{PAGENAME}} on other websites== | ||
Revision as of 05:01, 2 August 2006
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| T4-like genome database | |
| Who: | Jim Nolan
Tulane Univ. |
| What: | Genome information about T4-like bacteriophage |
| Where: | T4-like genome database |
| Updates | |
| Upcoming events | n/a |
| Web Services | |
About T4-like genome database
T4-like genome database is a site with genome browsers for the annotated genomes of a set of T4-like bacteriophage sequenced at Tulane and elsewhere.
Content
Genome data and GBrowse-based browsers for T4 family members Bacteriophage RB14, RB32, Acinetobacter phage 133, Aeromonas phage 25, Aeromonas phage 65, Vibrio phage nt-1, bacteriophage phi-1, RB16, RB43, Phage 31, 44RR2.8t, Aeh1, RB49, RB69, T4, P-SSM2, P-SSM4, S-PM2, KVP40. There is also a local BLAST for T4-like phage genomes and a forum for discussion of phage biology and genomics.
Using T4-like genome database
Browsing
The home page lists each of the phage genomes covered and links to their GBrowse pages, a more classic but noninteractive graphical map, FASTA files for proteins, RNAs, and genomes, and links to the NCBI browser and Genbank pages. Clicking on a gene in the browser brings up a summary page that has much more than the standard GBrowse data page. The data for each gene includes the DNA and protein sequences, statistics about the protein, a popup alignment viewer, and a White-Wimley hydropathy plot.
Tracks in the browser include BLAST hits to the other covered genomes. Clicking on these takes you to the browser for the other phage.
Searching
Searching is via the GBrowse search box
Usage examples
Technology
GBrowse plus analysis packages used to generate annoation tracks.
Web Services/API
GBrowse includes a Moby interface. Not documented whether it works on this site.
Discussion
References
External Links
T4-like genome database URL: http://phage.bioc.tulane.edu