ASGARD / News: Recent posts

Version 1.6.2a released

ASGARD v. 1.6.2a

This version simply corrects a few small bugs in the generation of the annotation table for long DNA sequences.

Also, the annotation table is now printed in lexical order, by contig identifier.

And finally, improved the GFF3 file created when input sequences are short (e.g. genes or proteins), by removing the repeated header and adding a note with the description of the BLAST match.... read more

Posted by J Alves 2014-03-17

Version 1.6.2 released

ASGARD v. 1.6.2

Version 1.6.2 is now available.

Version 1.6.2 introduces a couple of changes in how data was output to the .path_rec file, and one new feature: the annotation table (option -A).

Using -A, one can create a tab-delimited annotation table for all sequences that were input -- in the case of split contigs, the sequences will be the fragments, with contig name and BLAST match coordinates forming the identifier. For more detail, see the manual.... read more

Posted by J Alves 2014-03-14

Data downloader now working with new KEGG

Good news! After quite an interregnum, I was finally able to resume development of ASGARD, and the first and most pressing issue to be dealt with was the download_ASGARD_data, which had gotten broken when KEGG changed its access details after it became a subscription service.

Now, if your lab or institution has a subscription to KEGG's data, you should be able to use download_ASGARD_data to automatically download their data. Notice that you MUST be on a computer whose IP address is recognized by KEGG's server as being from a subscribing entity.... read more

Posted by J Alves 2014-03-07

New KEGG access mode and ASGARD

As some might have already noticed, access to KEGG's data through FTP is, since July 1st 2011, only available through subscription: http://www.genome.jp/kegg/docs/plea.html

That obviously breaks ASGARD's automated data download in a big way. Users will now need to:

1 - subscribe to KEGG
2 - manually download the data

From there on the formatting and use of the data should proceed as before, unless KEGG has changed their data structure again.... read more

Posted by J Alves 2011-07-07

Version 1.5.3 released

ASGARD 1.5.3 released

- Important bug fixed: KEGG data was being searched but not incorporated in the metabolic reconstruction.
- Added run logging to a file (ALOG_*.txt)
- Fixed a bug that was breaking GFF3 files created when using the -w option.
- And other small changes, typos, etc..

Posted by J Alves 2011-01-19

ASGARD 1.5 released

ASGARD version 1.5 has been released today after several tests were completed. See below for the main changes in the several components.

ASGARD v. 1.5

Updated: 2010-07-20

Changes from version 1.0.5:

- changes to download_ASGARD_data to:
* get KEGG orthology (KO) information
* get the new KEGG data structures (PNG maps intead of GIF, no more .coord files, etc.)
* other minor differences
- changes to format_ASGARD_data to:
* fixed a bug preventing the incorporation of ec2go information into sp2ec
* deal with KO information
* deal with compressed files
- changes to ASGARD to:
* read and/or create compressed files
* add progress reports during run
* allow the use of BLAST table reports with columns in different orders from the default
(for E-value only, for now; query and subject IDs still have to be the first two columns)
* changed generated GFF to version 3
* other minor updates
- changes to color_map to:
* read compressed files
* use KO information in addition to (or instead of) EC and GO
* deal with polygons used in some maps, e.g. the overall metabolim map (map01100)
* report pathways where there were differences detected (when analyzing more than one
dataset)
* other small tweaks to graphical presentation
- extensively changed the manual (LaTeX and PDF) to reflect all updates

Posted by J Alves 2010-08-03