AspGD Help: Batch Download

Contents

• Description
• Using the Batch Download Tool

Description

AspGD'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.

Using the Batch Download Tool

• Genomic DNA (DNA sequence of each feature, including introns)
• Genomic DNA plus any desired length (in basepairs) of upstream and/or downstream flanking sequence for each feature
• Coding Sequence of each feature (exons only)
• ORF translation - retrieves the translation of the coding sequence (i.e., protein sequence) for each protein-coding gene. Note that non-coding DNA features such as centromeres are not translated in this option.
• Chromosomal Coordinates - retrieves data on chromosomal features, similar to the 'chromosomal_feature.tab' file found on the AspGD Download site. The columns in this file are as follows.
  
  

  Column
  1) Feature name (mandatory); this is the primary ANxxxx 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 AspGDID
  10) Secondary AspGDID (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-Aspergillus mappings, are contained in the Ortholog and Best Hit file (see below).

  
  
  
• Gene Ontology (GO) Annotations - retrieves GO annotations for features, in the format of the 'gene_association.AspGD' file found on the AspGD Download site. This is the standard file format for gene_association files of the Gene Ontology (GO) Consortium. A more complete description of the file format can be found at the GO Consortium's website.
  The columns in this file are as follows.
  
  

  Column	Description
  1) DB	database contributing the file (always "AspGD" for this file)
  2) DB_Object_ID	AspGDID
  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 "AspGD" for this file)

  
  
  
  
• Phenotypes - retrieves phenotype data in the format of the 'A_nidulans_phenotype_data.tab' file found on the AspGD Download site. The columns in this file are:
  
  

  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) AspGDID (mandatory)	the AspGDID, unique database identifier, for the genomic feature
  5) Reference (AspGD_REF mandatory, PMID optional)	PMID:####|AspGD_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) Phenotype (mandatory)	Observed feature of the mutant strain, and the direction of change relative to wild type
  10) Chemical (optional)	Name of any chemicals used in the phenotype assay; additional details such as concentration may be in parentheses
  11) Condition (optional)	Conditions under which the phenotype was assayed, e.g., type of growth medium
  12) Details (optional)	Additional information relevant to the phenotype
  13) Reporter (optional)	The protein(s) or RNA(s) used in an experiment to track a process
  14) Anatomical structure (optional)	The Fungal Anatomy Ontology term that denotes the affected structure for an anatomical phenotype
  15) Virulence model	The model system used to assess the virulence of a mutant

  
  
  
• Orthologs and Best hits - retrieves Aspergillus and S. cerevisiae orthologs and best hits in a tab-delimited file format. See this description of the details on the method used to identify orthologs and best hits. The columns in this file are:
  
  

  Column	Contents
  1) ORF (mandatory)	Systematic name of the AspGD ORF
  2) Gene (optional)	AspGD standard gene name, if one exists
  3) ID (mandatory)	Unique database identifier, for the ortholog or best hit match
  4) Ortholog 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, see detailed description ).

  
  
  

Interpreting the results

Return to AspGD	Send a Message to the AspGD Curators