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PACdb Help Page

Updated 4/11/2005 [Updated supported ID types in Advanced Search: Restrict by Gene ID]

Help Contents:

Quick Search
Advanced Search
Homology Search
Genome Alignment
Retrieve Request
When you get "No data found"
Contact Us

Quick Search
The Quick Search box can be found in the header of most pages, and most prominently on the PACdb main page. Search term(s) can be a gene name, gene ID, EST Accession, protein ID, or organism name. 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 Sites - Returns 3'-processing site specific information
    • ESTs - Returns EST specific information
    • 3' UTR Sequence - Returns 3' UTR sequence and 3' UTR specific information
    • PolyA site flanking sequences - Returns genomic sequence flanking 3' processing site(s) and relavant information

    Restrict by Genetic Location:

    • Organism - Choose which organism or choose "All" to search across all organisms
    • Chromosome/Contig - Choose which chromosome or choose "Any chromosome" if this isn't important
    • User Specified Contig - Choose "User Specified Contig" in previous field (Chromosome/Contig) and then type in a contig name in the User Specified Contig text box
    • 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 and/or gene names
    • Number of PolyA sites (per gene) - Choose "One" for genes with only one PolyA site. Choose "Multiple" for genes with more than one PolyA site and choose "Any number" if the number of PolyA sites per gene isn't important.
    • PolyA site location (relative to CDS) - Choose "Internal" for genes with PolyA sites occuring between the start and stop codons (within the coding sequence). Choose "External" for genes with PolyA sites occuring in the UTR. Choose "Anywhere" if PolyA site location relative to CDS doesn't matter.
    • PolyA site confidence level - Allows the user to specify the confidence level(s) of data to return. Sorry, not fully supported at this time Confidence levels can be selected for individiual genes in PACdb's GeneView
    • 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 for A. thaliana
    • Ensembl IDs for Mouse, Rat, Zebrafish, Fugu, D. melanogaster,C. elegans, Human, Mosquito, Dog, Chicken, and Yeast
    • SGD IDs and SGD Systematic IDs for Yeast
    • TIGR Rice IDs and Rice Genome Project IDs for Rice
    • MGI IDs for Mouse

    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, PACdb issues a Request ID. Usually PACdb 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.


When you get "No data found"
If you get the "No data found" message, usually from the Advanced Search form, there are several things you can still do to try and find your data:
  • Make your search less specific: Try using very general, basic terms. Limit the number of terms used in your search. Use less options in the Advanced Search. Remember that GO information is not available for every gene.
  • Spelling: Check spelling of each of your terms and try valid alternative spellings if applicable.
  • Acronyms: Spell out each word rather than using acronyms and abbreviations. Acronyms can differ in different annotation sources and different organisms and are best avoided when possible.
Still getting the "No data found" message? PACdb currently annotates putative PolyA sites using EST to genome sequence alignment. Not every gene has EST sequence data, and some organisms have more ESTs than others.

If you'd like more help, please don't hesitate to contact us at  .


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