AtPACdb Help Page

Updated 4/07/2005

Help Contents:

Quick Search
Advanced Search
Homology Search
Genome Alignment
Retrieve Request
Contact Us


Quick Search

The Quick Search box can be found in the header of most pages, and most prominently on the AtPACdb main page. Search term(s) can be a gene name, gene ID, EST Accession, or protein ID. Using the Search Type drop down menu select whether you want to search for something that starts, ends, contains, or matches exactly your search term(s). Note that using 'contains' and 'ends with' can be slow (up to 22 seconds) due to the volume of data to search. However, using the 'starts with' or 'matches exactly' options takes usually less than a second. If you enter more than one search term and separate them with spaces or commas, Quick Search will return results that contain any of your search terms (a boolean OR). The Search Type drop down menu applies to all terms you've entered.


Advanced Search

Below are the help links for the major sections of the Advanced Search form:



    Retrieve:

    • Genes - this option brings back any gene(s) that matched the requested criteria provided by the user in the Advanced Search form.
    • PolyA Cleavage (PAC) Sites - Returns 3'-processing site specific information
    • ESTs - Returns EST specific information
    • 3' UTR Sequence - Returns 3' UTR sequence and 3' UTR specific information
    • PAC site flanking sequences - Returns genomic sequence flanking 3' processing site(s) and relavant information

    Restrict by Genetic Location:

    • Chromosome - Choose which chromosome or choose "Any chromosome" if this isn't important
    • Strand orientation - Choose which DNA strand (reverse/-/anti-sense or forward/+/sense) or choose "Either" if this isn't important

    Restrict by Gene Characteristics:

    • Keyword - based on GO annotations
    • Number of PAC sites (per gene) - Choose "One" for genes with only one PAC site. Choose "Multiple" for genes with more than one PAC site and choose "Any number" if the number of PAC sites per gene isn't important.
    • PAC site location (relative to CDS) - Choose "Internal" for genes with PAC sites occuring between the start and stop codons (within the coding sequence). Choose "External" for genes with PAC sites occuring in the UTR. Choose "Anywhere" if PAC site location relative to CDS doesn't matter.
    • PAC site confidence level - Allows the user to specify the confidence level(s) of data to return. Sorry, not fully supported at this time
    • Restrict by tissue type - actually a characteristic of the ESTs associated with the gene, enter a keyword, such as "seed" to show only genes containing ESTs with seen in this tissue type

    Restrict by Gene ID:

    In this text area you may enter one or more comma or space delimited IDs that are one of the supported types of gene IDs.
    Supported types:
    • TAIR ID (see http://www.arabidopsis.org)
    • GI - Genbank Identification number assigned by National Center for Biotechnology Information (NCBI)
    • Genbank Accession - assigned by NCBI

    Output formatting options:

    • Table - if your query returns a list of items, they will be displayed in an HTML table. if your query returns a single item, it will be displayed in a detailed HTML format.
    • XML - returns output in XML format
    • Tab delimited - returns output in tsv (tab separated values) format
    • FASTA - returns output in FASTA format (when appropriate)

Homology Search

The Homology Search form allows a user to enter a coding sequence (CDS) in either nucleotide or amino acid format, and then uses BLAST to find possible homologs.


Genome Alignment

The Genome Alignment form allows a user to enter any nucleotide or protein sequence, run that sequence through BLAT (for nucleotide) or tBLASTn (for protein), and then either view the raw alignment output, or get a list and visual depiction of genes and cleavage sites that overlap the alignment plus the 'radius'. The radius is is the distance upstream and downstream from the query's alignment that overlapping can occur. The radius can be zero, but is usually used to find potential 3'-processing sites downstream of an mRNA sequence query.


Retrieve Request

For potentially slow queries, AtPACdb issues a Request ID. Usually AtPACdb will forward you directly to your results and you don't need to keep your Request ID. However, if you'd like to refer back to your results up to 3 days after your query, enter your Request ID in the Retrieve Request form and you will be taken to the (temporary) URL where your results are located. Large requests may be deleted within 24 hours, all requests will be deleted after 3 days.


Contact Us

If you still have questions after reading through the help file, please don't hesitate to contact us at  .