Converting between annotated and featureless formats

The Set Full File Conversion default setting of natural causes SeqNinja to write/read only those items that are “natural” to the receiving/source file type. Changing the setting to full when changing from an annotated format to a featureless format and back again creates auxiliary file(s) to preserve features and comments that would otherwise be lost.

*Note: The conversion setting must appear in the script before the operation in which file output is specified.

Converting from GenBank and Lasergene (.seq) format to FASTA format:

“Full” can preserve features and comments that would normally be lost when converting from annotated format to FASTA format, then back again. However, “full” is not suggested in all cases; for instance, it is not recommended when you plan to make sequence modifications (other than substitutions) while the sequence is in FASTA format.

When “full” is selected, SeqNinja outputs three files during conversion from an annotated format to FASTA format:

• .fasta – This is a standard FASTA file containing sequence reads. When writing FASTA files from a source that contains comments, the FASTA header line includes the first line of comments from the source. For example:
  
  > NC_010473 LOCUS NC_010473 4686137 bp DNA circular BCT 04-OCT-2012

• .fasta.starff –This file contains tab-delimited feature information from the original annotated file and can be opened and modified using a spreadsheet utility such as Microsoft Excel®. The modified file can be read by SeqNinja, with the following restrictions: 1) Sequences must appear in exactly the same order as in the corresponding FASTA file. 2) The first six columns must remain present in the original order. Subsequent columns contain qualifier values named in the column header, and can be removed or amended, as desired.

• .fasta.comments – This file contains one comment pertaining to each sequence in the FASTA file, and in the same order.

*Note: Comments are maintained during file conversions (e.g., a.seq = b.gbk). However, comments are discarded during sequence transformations (e.g., a.gbk = b.gbk + c.gbk).

Converting the saved FASTA file back to GenBank or Lasergene format:

If you used full during the conversion to FASTA, you could convert back to GenBank or Lasergene, using full again, without losing the original features and comments. As long as you keep the auxiliary files in the same folder as the FASTA data file, SeqNinja will automatically place the features and comments back in the GenBank or Lasergene file.