Upload GenBank records

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GenBank Loader

Description
New GenBank records are imported automatically on a weekly basis. Check the GenBank Loader weekly to see if new records are in the database. See the criteria for reconciling GenBank records with a Gene Prediction.
dictyBase curator
  • Check to see that the GenBank record is aligning with the correct gene.
  • Check all information for accuracy and compatibility with existing information in the database.
  • Click 'Load' and information will be available on production.




Checking GenBank records

To determine whether a GenBank sequence should be reconciled with a Gene Prediction
  1. BLAST CDS of GenBank against all dictyBase CDS: Top hits should be itself and the Gene Prediction identified in the BLAST report; make sure the gene being linked is the best hit.
  2. Likewise, BLASTing the Gene Prediction against all dictyBase CDS should have the same top hits; all other hits should be insignificant.



Public notes for GenBank records

Description
This note may be used for any gene in which the Sequencing Center sequence has been compared to sequences in GenBank or EST sequences (gene may or may not have a Curated Model). Typically we do not report sequence differences in non-coding regions (introns and upstream/downstream sequences). Use the note that is most appropriate for the gene.
Notes
Note regarding this sequence: the sequences from the Sequencing Center and GenBank record [XXXXX] are identical.
[one GenBank record]


Note regarding this sequence: the sequences from the Sequencing Center and GenBank records [XXXXX] and [YYYYY] are identical.
[two or more GenBank records]


Note regarding this sequence: there is a discrepancy between the sequence from the Sequencing Center and the sequence in GenBank record [XXXXX], however, the sequence from the Sequencing Center has been verified.
[This note is used when two or more ESTs from independent libraries confirm the Sequencing Center sequence. Amino acid substitutions are not reported in this case. "Discrepancy" is always singular even if multiple nucleotide differences exist.]


Note regarding this sequence: there is a discrepancy between the sequence from the Sequencing Center and the EST sequences, however, the sequence from the Sequencing Center has been verified.
[This note is used when one of the Sequencing Centers (Jena or Baylor) confirm the Sequencing Center sequence. Amino acid substitutions are not reported in this case. "Discrepancy" is always singular even if multiple nucleotide differences exist.]


Note regarding this sequence: there is a(n) X nt difference between the sequence from the Sequencing Center and the sequence in GenBank record [XXXXX], resulting in X amino acid substitution(s) at position(s) Y and Z.


Note regarding this sequence: there is a(n) X nt difference between the sequence from the Sequencing Center and the sequence in GenBank record [XXXXX]; the encoded proteins are identical.




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