dictyBase Help: Sequence Info Page

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Contents

• Description
• Content of the Sequence Info Page
• General Information
• Sequences Retrieval and Analysis
• Protein Information
• Sequences
• References
• Relevant dictyBase Help Documents
• Relevant dictyBase Glossary Terms

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Description

Every sequence associated to a gene has its own Sequence Info Page. This includes curated models, gene predictions, and GenBank sequences (including ESTs). Translated sequences include the protein sequences. The Sequence Info Page also provides a portal for submission to a BLAST search.

Content of the Sequence Info Page

The dictyBase Sequence Info Page is divided into several sub-sections. The different sections are preceded by a line of Navigation Links:

The last, red marked item in this navigation list informs you on which page you currently are. The dictyBaseID indicates you are on a Sequence Info Page, the preceding gene name indicates the gene to which this sequence is associated. By clicking on the 'Chromosome' link you navigate to the Genome Browser.

• General Information

• This section describes the source of the sequence and shows a mini map with coordinates.

  • Feature Type
    The Feature Type describes the origin of the sequence displayed on the page. Feature Types include Curated Model, Gene Prediction From Sequencing Center, Genomic Fragment, mRNA, or EST.
  • Map
    Sequence Info Pages for Curated Models and Gene Predictions have mini maps that also serve as a link to the Genome Browser. The chromosomal coordinates are on the right of the minimap.

• Sequence Retrieval and Analysis

• This section serves to retrieve an BLAST sequences.

  The sequence available for retrieval depends on the Feature Type. Only Sequence Info Pages for Curated Models, Gene Predictions, and GenBank Genomic Fragments and mRNAs have different options for sequence retrieval (typically options 1, 2, and 3 or 4):

  1. Protein
  2. DNA Coding Sequence
  3. Genomic DNA
  4. mRNA sequence

  Clicking on the sequence retrieves the sequence; clicking the button next to the sequence determines which sequence will be subjected to a BLAST search. From the BLAST options BLASTN or BLASTP will be automatically chosen depending on the selected sequence (DNA or protein). BLAST options link to the dictyBase BLAST server (BLASTN, BLASTX, TBLASTN, TBLASTX, BLASTP), or directly to NCBI BLASTP. For more information on BLAST refer to the BLAST Help Page.

• Protein Information

• This field provides protein data such as the length and molecular weight calculations. The Amino Acid Composition link opens in a pop-up window. Information about protein structure will be available in the future.

• Sequences

• The Sequences section contains all available sequences for a given feature. This may be the sequences as listed under Sequence Retrieval and Analysis, or just one sequence in the case of EST features.

• References

• This section lists the reference(s) associated to the sequence source.

Relevant dictyBase Help Documents

• BLAST
• Gene Page
• Genome Browser

Relevant dictyBase Glossary Terms

• Curated Model
• EST
• Gene Name
• Standard Name
• BLAST
• FASTA
• GenBank