SGD 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
• Glossary Terms

Description

Gene/Sequence Resources (GSR) serves as a central point for accessing much of the information available at SGD for a 1) a named DNA sequence, 2) a specified chromosomal region, or 3) a raw DNA or protein sequence. This information includes biological information, table/map displays, and sequence analysis and retrieval options. Once you have specified a sequence name or region, GSR will present only those options which are available for obtaining information about your entry.

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 (i.e. BLAST, FASTA, Restriction Analysis).

Using Gene/Sequence Resources

• Pick a Sequence Query Option

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

  • 1. Enter a named DNA sequence

    With this input option, you can enter a gene name, a GenBank sequence name or accession number, an ORF name, or an ATCC or WashU clone name. 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.

    If you would like to retrieve or manipulate the reverse complement of the sequence, check the "Use the Reverse Complement" box.

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

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

    

    
    

  • 2. Pick a chromosome

    This entry option allows you to specify a region by entering the desired chromosome number and coordinates. To use this option, simply select a chromosome number using the pull-down menu, and then enter the left and right chromosomal basepair coordinates in the boxes provided below. If you do not specify the basepair coordinates, the first 100,000 basepairs will be displayed.

    If you would like to retrieve or manipulate the reverse complement of the sequence, check the "Use the Reverse Complement" box OR enter the coordinates as the Note suggests.

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

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

    

    
    

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

    This entry option allows you to specify 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).

    If you would like to analyze the reverse complement of the sequence you entered, check the box next to "Use the reverse complement" located below the sequence entry box.

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

    Select "Submit form" to bring up the list of 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 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 page corresponding to the name of the gene or ORF name you originally entered. This page provides information, when available, about observed phenotype(s), sequence coordinates, as well as links to protein info, homolog comparison resources, literature, maps, expression in microarray datasets, PIR, MIPS, and SwissProt and more. [SGD 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 name. The Literature Guide is a categorization of journal articles for a specific gene or ORF name into various biological topics based on the contents of the abstract.
        [SGD Help: Literature Topics]

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

        
        

     3. Sequence Details: This link goes to the Sequence class of information for an entered sequence name. In the case of a gene or ORF name, the sequence information for the ORF is provided. [SGD Help: Sequence Names]

        Availability: This option is available when a GenBank name, or an accession number is entered on the Gene/Sequence Resources entry page.

        
        

     4. Clone details: This link goes to the Clone class of information for the entered sequence name. Within the SGD database, a Clone is defined as a piece of DNA that has been placed on the physical map by sequence alignment or by nucleotide hybridization experiments.
        [SGD Help: Clone]

        Availability: This option is available when an ATCC or WashU clone name is entered on the Gene/Sequence Resources entry page.

        
        

     5. Protein Info: This link goes to the Protein Page for an entered gene or ORF name. Protein pages contain information about the gene product, such as length (in aa), predicted molecular weight, codon bias, and links to motif information, protein chemistry, protein structure and homologs. This information is calculated by SGD or derived from the GCG package. See the Help document associated with the Protein page for more information.

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

        
        

     6. 3-D Structure (formerly linked to Sacch3D): This link goes to PDB Homologs Resource for the gene entered on the query page. The PDB Homologs page presents information for the proteins of known structure with sequence similarity to the specified Saccharomyces cerevisiae protein. The results will display both the yeast protein structure (if it has been solved) and the structure of other related proteins (regardless of sequence source).
        [PDB Homologs Help]

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

        
        

     7. Global Gene Hunter: This link goes to a Global Gene Hunter form which is already filled out with the desired gene or ORF name. Global Gene Hunter allows you to simultaneously search for information on a gene or ORF name in any or all of seven different databases. [SGD Help: Global Gene Hunter]

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

        
        

     8. Mammalian Homologs: This link takes you directly to the results of a BLASTP against mammalian protein sequences in GenBank where the query was the gene product of the name you entered. [BLAST Help]

        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. Chromosomal Features Map: This links to a graphic representation of the genetic features of a region of chromosomal DNA around the selected gene or ORF. These features include ORFs, RNA genes, centromeres and Ty elements. [SGD Help: Chromosomal Features Map]

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

        
        

     2. Chromosomal Features Table: This option links to a table listing the sequence features in the same region as the query gene. The type of feature, the strand on which the sequence is contained, and the chromosomal coordinates are given in the Feature Table. For more information see the [SGD Help: Chromosomal Features Table]

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

        
        

     3. Combined Physical and Genetic Map: This link goes directly to the Combined Physical and Genetic Map around the entered gene or ORF, which is a side by side representation of the physical and genetic maps for the chromosome. It contains genetically and/or physcially mapped ORFs. [SGD Help: Combined Physical and Genetic Map]

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

        
        

     4. Physical Map: This links to the Physical Map around the selected gene or ORF. It shows the location of all the genetic elements available via the Chromosomal Features Map and, in addition, shows the locations of overlapping ATCC clones. [SGD Help: Chromosomal Physical Map]

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

        
        

     5. Genetic Distance vs. Physical Distance Ratios: This links to the Genetic Distance vs. Physical Distance Ratios Map around the entered sequence name. These ratios are calculations based on data in SGD. Genetic distance (in centimorgans) is divided by the physical distance (in kilobasepairs) and graphed along the length of the chromosome. [SGD Help: Genetic Distance vs. Physical Distance Ratios]

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

        
        

     6. Genomic Stripe View: This links to a display of all regions in the genome which are similar to an entered gene or ORF name. [SGD Help: Genomic Stripe View]

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

  3. Sequence Analysis
     1. BLAST Search: This links to a SGD 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. [SGD Help: BLAST Searches]

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

        
        

     2. FASTA Search: This links to a SGD FASTA 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. [SGD Help: FASTA Searches]

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

        
        

     3. Genome Restriction Map: This links to the Yeast Genome 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. [SGD Help: Yeast Genome Restriction Analysis]

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

        
        

     4. Design Primers: This links the Design Primer feature, with the selected DNA sequence already pasted in. Design Primers locates primers for PCR or sequencing of an entered sequence based on specified parameters. [SGD Help: Design Primers]

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

        
        

     5. Genome Pattern Matching: This links to the Yeast Genome Pattern Matching feature, with the raw DNA or protein sequence you entered already pasted in. Yeast Genome Pattern Matching allows you to search for short (<20 residues) nucleotide or peptide sequences, or ambiguous/degenerate patterns (use BLAST or FASTA for searches using >20 residues). [SGD Help: Pattern Matching]

        Availability: This option is available when either raw DNA or raw protein sequence is entered on the Gene/Sequence Resources page.

        
        

     6. Translated Protein Sequence: This option allows you to obtain the translated protein sequence when you enter a raw DNA sequence on the Gene/Sequence Resources entry page (option 3). Directly below the translated sequence you obtain, is the option to do a BLAST and a FASTA search on the translation, with the amino acid sequence pre-pasted onto the BLAST or FASTA form.

        Availability: This option is available when raw DNA sequence is entered on the Gene/Sequence Resources page.

        
        

  4. Sequence Retrieval
     1. DNA of Region (with introns): Selecting either GCG, FASTA, or NoHeader brings back the DNA of the selected sequence, including any introns, in whichever of the 3 output formats you select.

        Availability: This option is available when a gene name, ORF name, ATCC or WashU clone name, GenBank name, accession number, or a chromosomal region is entered on the Gene/Sequence Resources page.

        
        

     2. Coding Sequence of selected gene/ORF (without introns, without flanking regions): Selecting either GCG, FASTA, or no Header brings back the DNA of the selected sequence, without introns or flanking regions, 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.

        
        

     3. Protein Translation: Selecting either GCG, FASTA, or NoHeader brings back the protein translation of the selected sequence in whichever of the 3 output formats you select.

        Availability: This option is available when a ATCC or WashU clone name, GenBank name, accession number, or a chromosomal region is entered on the Gene/Sequence Resources page.

        
        

     4. 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.

        
        

     5. 6-Frame Translation (with Restriction Map): Clicking on GCG brings back a 6-Frame Translation of the selected sequence in GCG format. This translation is accompanied by the DNA sequence with a restriction map and is generated at SGD using a licensed version of the Wisconsin Sequence Analysis Package® from the Genetics Computer Group.

        Availability: This option is available when a gene name, ORF name, ATCC or WashU clone name, GenBank name, accession number, or a chromosomal region is entered on the Gene/Sequence Resources page.

        
        

     6. Restriction Fragment Sizes: Clicking on GCG gives restriction fragment sizes for the selected sequence. This display is generated at SGD using a licensed version of the Wisconsin Sequence Analysis Package® from the Genetics Computer Group.

        Availability: This option is available when a gene name, ORF name, ATCC or WashU clone name, GenBank name, accession number, or a chromosomal region is entered on the Gene/Sequence Resources 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 SGD generate DNA alignments between similar S. cerevisiae DNA sequences. If you are interested in retreiving the sequence of the 'subject' gene, the chromosomal coordinates of the subject sequence are given at the top of the alignment. You paste these numbers into the GSR tool. (Remember to note the chromosome!) You can also go to the Locus page of the 'subject' gene and get the coordinates there.
• The Chromosomal Features Table contains a list of sequence features (ORFs, Ty Elements, CENs, ARSs, and etc) and their chromosomal coordinates for a region. The chromosomal Feature Table is generated in Gene/Sequence Resources when a gene, ORF, ATCC number, or WashU clone name is queried. For more information see the [SGD Help: Chromosomal Features Table]

Accessing Gene/Sequence Resources

• Selecting Gene/Sequence Resources from any toolbar at the top of a page, the left hand navigation bar of any resource page, or on the Analysis & Tools resource page.
• Selecting Gene/Sequence Resources at the bottom of any Genomic View page, any Chromosomal Features Map display page, any Chromosomal Features Table page, any Physical Map page, or any Genome-wide DNA Similarity View page.
• Selecting the Gene/Sequence Resources link on numerous SGD database pages

Other Relevant Links

• Global Gene Hunter
• Search SGD

Associated Glossary Terms:

• Accession number
• ATCC
• Coding Sequences (cds)
• GenBank
• Gene Name
• ORF
• Physical Map
• Sequence
• Sequence features

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