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CGD's Batch Download tool and Gene/Sequence Resources 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 Batch Download retrieves only the sequences of the features (protein-coding and RNA genes, centromeres, etc.) that are annotated within the specified region(s), while Gene/Sequence Resources retrieves the entire nucleotide sequence between the coordinates specified in a list.
The data that can be retrieved using this tool are also found in files available at our Download site.
chromosome_number or contig_number[tab]start_coordinate[tab]stop_coordinateIf no coordinates are entered, all the features in the selected chromosome or contig will be retrieved.
Note that this option will not retrieve data for features that are
partially within and partially outside of the input coordinates.
The name of the strain must also be chosen (from the pull-down menu) as part of the input to the Batch Download tool.
| Column |
|---|
| 1) Feature name (mandatory); for C. albicans this is the primary orf19 name, if available |
| 2) Standard gene name (locus name) |
| 3) Aliases (multiples separated by |) |
| 4) Feature type |
| 5) Chromosome |
| 6) Start_coordinate |
| 7) Stop_coordinate |
| 8) Strand |
| 9) Primary CGDID |
| 10) Secondary CGDID (if any) |
| 11) Description |
| 12) Date Created |
| 13) Sequence Coordinate Version Date (if any) |
| 14-15) Blank |
| 16) Date of gene name reservation (if any) |
| 17) Has the reserved gene name become the standard name? (Y/N) |
| 18) Name of S. cerevisiae ortholog(s) (multiples separated by |); please note that this file only contains the S. cerevisiae ortholog(s); all orthologs and Best Hits, including inter-Candida mappings, are contained in the Ortholog and Best Hit file (see below). |
| Column | Description |
|---|---|
| 1) DB | database contributing the file (always "CGD" for this file) |
| 2) DB_Object_ID | CGDID |
| 3) DB_Object_Symbol | see below |
| 4) NOT (optional) | 'NOT' qualifier for a GO annotation, when needed |
| 5) GO ID | unique numeric identifier for the GO term |
| 6) DB:Reference(|DB:Reference) | the reference associated with the GO annotation |
| 7) Evidence | the evidence code for the GO annotation |
| 8) With (or) From (optional) | any With or From qualifier for the GO annotation |
| 9) Aspect | which ontology the GO term belongs in |
| 10) DB_Object_Name(|Name) (optional) | a name for the gene product in words, e.g. 'acid phosphatase' |
| 11) DB_Object_Synonym(|Synonym) (optional) | see below |
| 12) DB_Object_Type | type of object annotated, e.g. gene, protein, etc. |
| 13) taxon(|taxon) | taxonomic identifier of species encoding gene product |
| 14) Date | date GO annotation was made |
| 15) Assigned_by | source of the annotation (always "CGD" for this file) |
| Column | Contents |
|---|---|
| 1) Feature name (mandatory) | Systematic name of the genomic feature |
| 2) Feature type (mandatory) | Type of genomic feature, e.g., ORF |
| 3) Gene (optional) | Gene name, if one exists |
| 4) CGDID (mandatory) | The CGDID, unique database identifier, for the genomic feature |
| 5) Reference (CGD_REF mandatory, PMID optional) | PMID: ####|CGD_REF: #### (separated by pipe)(one reference per row) |
| 6) Experiment type (mandatory) | Type of experiment used to detect the phenotype; additional comments may be in parentheses |
| 7) Mutant type (mandatory) | Classification of the effect that the mutation has on the gene product, e.g., "null", "conditional" |
| 8) Allele (optional) | Name of the mutant allele; additional information such as the amino acid affected may be in parentheses |
| 9) Strain background (mandatory) | Genetic background in which the phenotype was analyzed |
| 10) Phenotype (mandatory) | Observed feature of the mutant strain, and the direction of change relative to wild type |
| 11) Chemical (optional) | Name of any chemicals used in the phenotype assay; additional details such as concentration may be in parentheses |
| 12) Condition (optional) | Conditions under which the phenotype was assayed, e.g., type of growth medium |
| 13) Details (optional) | Additional information relevant to the phenotype |
| 14) Reporter (optional) | The protein(s) or RNA(s) used in an experiment to track a process |
| 15) Anatomical structure (optional) | The Fungal Anatomy Ontology term that denotes the affected structure for an anatomical phenotype |
| 16) Virulence model (optional) | The model system used to assess the virulence of a mutant |
| Column | Contents |
|---|---|
| 1) ORF (mandatory) | Systematic name of the CGD ORF |
| 2) Gene (optional) | CGD standard gene name, if one exists |
| 3) CGDID/SGDID (mandatory) | CGDID or SGDID, unique database identifier, for the ortholog or best hit match |
| 4) Gene Name (mandatory) | Standard gene name or systematic name of the ortholog or best hit match |
| 5) Ortholog or Best hit? (mandatory) | Indication whether the gene is an ortholog or whether it is a best hit (lower stringency match in cases where there is no match that meets the strict orthology criteria |
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