Help! How do I use this web site?
The yellow menu frame on the left side of window stays in place for all of the pages on this site and contains links to the main areas of the site - think of it as a menu. Any time you're in the RNase P Database, you can click on any of the items on the menu to go jump directly to that section.
At the top of the 'menu' is a link to the site Home page, the main doorway to the site. This page is essentially a Table of Contents, and often also contains timely annoucements and other useful information.
The Help page is a collection of additional helpful information on how to use this site, including basic 'How to use this site' (this page!), file formats information, etc.
If you're new to the database, start with the Information page. This page contains contact information for the database, basic information about the database and RNase P, and a bibliography of RNase P publications. There is also a link to a computer software page, containing a variety of free software of use to those of us in the RNA world. Also on this page is a link to a list of Worldwide Web sites that might be of use to users of the database.
The What's New? page contains a list of new data, changes & updates, and other timely information. Routine users of the database will find this a very useful 'first stop', since each of the listings is linked directly to the appropriate place in the database.
The Sequences & Structures page is a list of organisms with information in the database, arranged in phylogenetic groups. Each of these phylogenetic groups has its own page, and can be accessed by clicking on the name of the group. Clicking on a genus name takes you to the appropriate page and, if that page is a long one, to the place on that page where the data for that genus is. Near the top of the page, below the 'RNase P Database' header, are links to the 'Prior page' and 'Next page' - click on these to browse the individual pages; the order of the pages is the same as on the main Sequences & Structures page.
Each of the sequences & structures sub-pages contains a tablewith rows arranged like this:
Genusbacterium specii Strain X12345 Doe, J., et al, 1914 Science 94:123 E. pluribus (unum) AL43210 Jefferson, et al, unpublished
The first column usually contains the names of organisms by genus & species. Species names are linked to the NCBI/Entrez Taxonomy record for that organism - click on the name to get more information about the organism or look for other publications or sequences from that organism. In instances where the organisms a sequence comes from is unknown (e.g. 'natural populations' or contaminants sequences), clone designations are given.
The next column is the strain of that species. If that specific strain contains an entry in the NCBI Taxonomy Browser, then the strain name is linked to that record.
The next column contains the Genbank accession number for the sequence. Clicking on this number will take you to the official sequence record via NCBI/Entrez. More often than not, the Genbank sequence record is more than just the RNase P sequence, usually the entire continuous sequence that was determined - in some cases, it might be the entire genome sequence of that organism! If the sequence is not in Genbank, there will be an 'under construction' marker in this place.
The net column contains a set of buttons for accessing data. The button will show you the sequence of the RNase P RNA, in Genbank format. The button is linked to a file containing the secondary structure of the RNA in Connect format, with pseudoknots not allowed. The button is linked to a similar Connect file in which pseudoknots are included. The button gives you the RNA secondary structure in RNAML (a.k.a. RiboML, a.k.a. the Madison format). Most of the secondary structures are also available for viewing directly in your browser in Adobe Acrobat format ( or ). If these file formats are not familiar to you, a brief description of each is available on the File types page. If the sequence is a protein rather than an RNA, the button will show you the amino-acid sequence in GenBank format. If you want the DNA sequence encoding this protein, use the Genbank accession link.
The last column gives the sequence citation. This citation is for the nucleotide sequence except where the sequence and secondary structures are listed on separate lines. Whenever possible, this citation is linked to its Medline record - click on the citation to go to that record via NCBI/Entrez.
The next set of links in the menu are the other main areas of the database: Alignments, 3D Models, and Stock Images areas. Each of these areas contains a list similar to that in the 'Sequence & Structures' section with available files.
The last menu choice is for the Brown Lab, where you can get all the information you want about the lab that administers this web site.
Still can't figure it out? Contact me by e-mail at : firstname.lastname@example.org.
Last updated by JWBrown
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