CGD Help: Gene/Sequence Resources

Contents

• Description
• Using Gene/Sequence Resources
  • Sequence Query Options
  • Choose Result to View
• Finding Chromosomal Coordinates
• Accessing Gene/Sequence Resources
• Other Relevant Links

Description

CGD's Gene/Sequence Resources tool and Batch Download tool both allow you to retrieve sequences in batch for a list of regions. The difference between the batch options of these two tools is that GSR retrieves the entire nucleotide sequence between the coordinates specified in a list, while Batch Download retrieves only the sequences of the features (protein-coding and RNA genes, centromeres, etc.) that are annotated within the specified regions.

Whenever possible, selecting one of the available options for your entered sequence name or region takes you directly to the results for your entered sequence. In other cases, it takes you directly to the resource with the sequence already pre-pasted (e.g., BLAST, Restriction Analysis). When a list of sequence regions is entered, you will be presented with a link allowing you to download a file containing the sequences.

Using Gene/Sequence Resources

• Pick a Sequence Query Option

  Note: Only ONE of the options listed below may be filled out at a time in order for the submission to be processed.

  If at any time you decide you would like to change your selection, you may use the "Reset Form" button found at the bottom of the page to erase your entries.

  All of the options retrieve the Watson strand (with ascending chromosomal coordinates) of the specified gene or region. To retrieve the Crick strand, click the "Use the reverse complement" checkbox for that option.

  • Option 1. Enter a named DNA sequence

    With this input option, you can enter a gene name (e.g., ACT1), ORF name (e.g., orf19.5007), or a CGDID (e.g., CAL0001571). After you've entered the sequence name, click the "Submit form" button. Note that you can also enter the first few characters of a named DNA sequence followed by the wildcard character (*). Submit the query. Queries that match multiple names will return a list of sequences from which you can then select a single sequence.

    You may also retrieve information about flanking sequences upstream and/or downstream of the entered gene/sequence name. To do this, type the length of the flanking region you would like to retrieve in the boxes (upstream and/or downstream) below where you entered the sequence name. Note: negative numbers are not accepted in these boxes. If you would like to retrieve part of an ORF you should use the chromosomal coordinates in retrieval option 2.

    Select "Submit form" to bring up the list of further options available for viewing and retrieving information about the named sequence you entered.

  • Option 2a. Pick a chromosome or contig

    This entry option allows you to specify a region by choosing the chromosome number or contig name from the pull-down menu and entering coordinates, if desired. To use this option, simply select a chromosome or contig using the pull-down menu, and then enter the left and right chromosomal basepair coordinates in the boxes provided below. If no coordinates are entered, the first 100,000 bp of the chromosome or contig will be retrieved.

    This option will retrieve the Watson strand, regardless of the order in which the coordinates are entered. If you would like to retrieve or manipulate the reverse complement of the sequence, check the "Use the Reverse Complement" box.

    Select "Submit form" to bring up the list of further options available for viewing and retrieving information about the sequence you selected.

    Note that the entire sequences of the chromosomes and contigs are also available for download from CGD's Sequence Download directory.

  • Option 2b. Upload a file of chromosome (or contig) regions

    If you would like to retrieve DNA sequences from multiple regions, create a file with the tab- or space-separated columns:

    1. chromosome/contig name
    2. start coordinate
    3. stop coordinate

    For example:

    Ca21chr3_C_albicans_SC5314   1356  20455
    Ca21chr4_C_albicans_SC5314  11331  18001
    Ca21chr6_C_albicans_SC5314   9856  100010
    
    Contig19-10109     4600    24000
    Contig19-10216  200310  220546
    

    Sequence coordinates (columns 2 and 3) are optional in this file; if no coordinates are present, the first 100,000 nucleotides of the chromosome or contig will be retrieved.

    Use the "Browse" button to locate the file on your computer and click the Submit button to upload it. The resulting page presents a link allowing you to download a compressed file in FASTA format containing the sequences you requested.

  • Option 3. Type or paste a raw DNA or protein sequence

    This entry option allows you to enter a raw DNA or protein sequence for which you would like to retrieve information. First, use the pull-down menu to select the type of sequence you would like to enter, DNA or protein. Next, position the cursor in the entry box and either type or paste in a sequence.

    Note that the sequence entered must be provided in RAW format, without comments (numbers are okay).

    Select "Submit form" to bring up the list of further options available for viewing and retrieving information about the named sequence you entered.

  • Choose Result to View

    After you submit either 1) a named sequence 2) a chromosomal region or list of regions, or 3) a raw DNA or protein sequence, a page is returned that lists all available information, displays, analyses, and sequence retrieval options available for the sequence. You will choose one of these options. Descriptions for each option are below. Please note that some of them may not be available for your selected entry, depending on the type of sequence you have entered.

    If you decide you would like to change your original selection, hit the button [Change Selection or Coordinates]. This will bring back the Gene/Sequence Resources entry page with your information still filled in. You can then modify and re-submit the form.

    1. Biology/Literature

       1. Locus info: This link takes you to the Locus Summary page corresponding to the gene or ORF whose name you originally entered, which provides information curated from the literature about that gene and its encoded product. [CGD Help: Locus]

          Availability: This option is available when a gene or ORF name is entered on the Gene/Sequence Resources entry page.

       2. Literature Summaries: This link takes you the the Literature Guide for an entered gene or ORF. The Literature Guide is a categorization of journal articles about a specific gene or ORF into various biological topics.
          [CGD Help: Literature Topics]

          Availability: This option is available when a gene or ORF name is entered on the Gene/Sequence Resources entry page.

    2. Display Maps/Tables

       1. GBrowse: This links to a graphical representation of the genetic features of a region of chromosomal DNA around the selected gene or ORF, from which the entire chromosome or contig may be navigated. [CGD Help: GBrowse]

          Availability: This option is available when a gene, ORF, or chromosomal region is entered.

       2. Flanking Features Table: This option links to a table listing the sequence features in the same region as the query gene. The name and aliases for each feature, the chromosomal coordinates, and feature descriptions are given in the Feature Table. Multiple data download options are available. For more information see the [CGD Help: Batch Download]

          Availability: This option is available when a gene, ORF, or chromosomal region is entered.

    3. Sequence Analysis
       1. BLAST Search: This links to a CGD BLAST form in which the query sequence is already pasted. One can then select the desired dataset and search options, and then submit the search form. [CGD Help: BLAST Searches]

          Availability: This option is available when a gene name, ORF, chromosomal region, raw DNA sequence, or raw protein sequence is entered on the Gene/Sequence Resources page.

       2. Genome Restriction Map: This links to the CGD Restriction Analysis feature, with the sequence you entered already pasted in. You may then select all or a specified set of restriction enzymes with which to generate the Restriction Map. [CGD Help: Candida Genome Restriction Analysis]

          Availability: This option is available when a gene name, ORF, chromosomal region, or raw DNA sequence is entered on the Gene/Sequence Resources page.

       3. Design Primers: This links to the Web Primer program, with the selected DNA sequence already pasted in. This tool locates primers for PCR or sequencing of an entered sequence based on specified parameters. [CGD Help: Design Primers]

          Availability: This option is available when a gene name, ORF, chromosomal region, or raw DNA sequence is entered on the Gene/Sequence Resources page.

    4. Sequence Retrieval
       1. DNA of Region: Selecting either GCG, FASTA, NoHeader or Decorated FASTA brings back the DNA of the selected sequence, including any intron/adjustment/gap regions, in whichever of the 4 output formats you select.
          

          The Decorated FASTA format is generated by GBrowse and shows sequence features by using various color schemes. The following sequence features are highlighted with the associated decorations as described below:

          • Exons of Protein-coding genes : Red font
          • Exons of Non-coding genes : Blue font
          • 5' UTR introns : Underline
          • Telomeres and Centromere : Tan background color
          • Transposons and Repeats : Grey background color
          • SNPs : Bold

          Availability: This option is available when a gene or ORF name or chromosomal region is entered on the Gene/Sequence Resources page.

       2. Exon(s) only Sequence of selected gene/ORF (without introns/adjustments/gaps): Selecting either GCG, FASTA, NoHeader or Numbered Sequence brings back the DNA of the selected sequence, without intron/adjustments/gaps, in whichever of the 4 output formats you select.
          The Numbered Sequence format shows the position of nucleotides within the sequence and also includes 200 bp upstream and downstream flanking regions. The core portion of the sequence (excluding the flanking regions) is separated by spaces into sets of 3 nucleotide bases. The sequence position counting for the flanking and the core sequence regions is done separately.

          Availability: This option is available when a gene name or ORF is entered on the Gene/Sequence Resources entry page.

       3. Protein Translation of ORF: Selecting either GCG, FASTA, or NoHeader brings back the protein translation of the selected gene or ORF sequence (using the first reading frame) in whichever of the 3 output formats you select.

          Availability: This option is available when a gene or ORF name is entered on the Gene/Sequence Resources entry page.

  Finding Chromosomal Coordinates

  • Chromosomal coordinates for ORFs are found on the Locus pages in the Sequence Coordinates section on the left side. The boundaries for introns (if present) and exons are listed here.
  • BLASTn reports at CGD generate DNA alignments between similar Candida DNA sequences. If you would like to retrieve the sequence of the 'subject' gene, you can copy the chromosomal coordinates of the subject sequence from the top of the alignment and paste these numbers into the GSR tool. (Remember to note the chromosome!) You can also go to the Locus Summary page of the 'subject' gene and get the coordinates there.
  • The Chromosomal Features Table contains a list of sequence features (ORFs, RNA-coding genes, centromeres, etc.) and their chromosomal coordinates for a region. For more information see the [CGD Help: Chromosomal Features Table]

  Accessing Gene/Sequence Resources

  Links to Gene/Sequence Resources are located in:
  • the toolbar at the top of most CGD pages;
  • the left-hand navigation bar on the CGD home page and on the pages listing CGD resources
  • the list on the Search Options index page

  Other Relevant Links

  • Search CGD

  Go to Gene/Sequence Resources

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