The Fragment Recruitment Viewer is currently not generating images properly. We would advise against running any FRV jobs until this has been resolved. (posted Feb 18, 2010 10:32)

FYI: In Firefox 3.6, some menus are not accessible in the CAMERA applications. For now, we recommend using Firefox 3.5.x. Also, if you are using IE8, please turn on "IE7 compatibility mode".

Thank you for your understanding.

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Release Notes - v.1.3.2

NCBI Update - CAMERA's Non-Identical Nucleotide Sequences (N)

January 4, 2009

Before the Update After the Update Increase
103,306,949,106 bp 179,511,589,666 bp + 76,204,640,560 / + 74%
21,668,450 seq 38,512,986 seq + 16,844,536 / + 78%

 

 

Version 1.3.2.29 Release Notes

May 11, 2009

  • Improvements
    • Job queueing system has been updated
    • Moore 150 data no longer redirects to Moore site
    • Default row count raised to 20 for projects page
  • Fixed Issues
    • Incorrect program choices (BLAST) - resolved
    • Verbiage changed for specifying query sequences to note that the FRV Blast is nucleotide only
    • Publications pages revised to show download links for projects without publications
    • Excel exports revised to properly show exponent values for e-values.
    • Excel exports - Habitat field removed (redundant with Site field)
    • Advanced BLAST - can now select a program if dataset selected before specifying query sequence

 

 

Moore 150 Update

March 6, 2009

  Before
the Update		 After
the Update		 Increase
Strains listed in the sample page 125 144 19
Strains which have available sequences 113 133 20
Sequences in the MF150 Genomes BLAST dataset 11,703 12,819 1,116
Total sequence length of the MF150 Genomes BLAST dataset 769,200,384 852,297,365 83,096,981
Sequences in the MF150 Peptides BLAST dataset 230,454 293,532 63,078
Total sequence length of the MF150 Peptides BLAST dataset 71,174,432 91,156,323 19,981,891

New organisms

organism taxon_id
Roseobacter sp. 391593
Unnamed Rhodobacterales bacterium 439496
Sagittula stellata 388399
Unnamed Rhodobacterales bacterium 314270
Octadecabacter antarcticus 391616
Roseobacter litoralis 391595
Phaeobacter gallaeciensis 391619
Unnamed Rhodobacterales bacterium 388401
Candidatus "Pelagibacter" sp. 439493
Unnamed Methylophilales bacterium 383631
Cyanobium sp. 180281
Bacillus sp. 388400
Algoriphagus sp. 388413
Methylophaga sp. 392484
Unnamed gammaproteobacterium 391615
Vibrio parahaemolyticus 391586
Unnamed gammaproteobacterium 566466
Lentisphaera araneosa 313628

Updated organisms

organism taxon_id
Algoriphagus sp. 388413
Bacillus sp. 388400
Caldanaerobacter DSM 12653 391606
Cyanobium sp. 180281
Erythrobacter litoralis 314225
Unnamed gammaproteobacterium 391615
Lentisphaera araneosa 313628
Unnamed Methylophilales bacterium 383631
Methylophaga sp. 392484
Marinitoga piezophila KA3 443254
Nitrosococcus oceani AFC-27 473788
Unnamed gammaproteobacterium 566466
Octadecabacter antarcticus 391616
Rhodobacterales bacterium HTCC2255 373154
Candidatus "Pelagibacter" sp. 439493
Unnamed Rhodobacterales bacterium 314270
Unnamed Rhodobacterales bacterium 388401
Unnamed Rhodobacterales bacterium 439496
Roseobacter sp. 391593
Phaeobacter gallaeciensis 391619
Roseobacter litoralis 391595
Sagittula stellata 388399
Vibrio parahaemolyticus 391586

Version 1.3.2.28 Release Notes

January 26, 2009

  • Fixed Issues
    • BLAST Result sorting - In this release, the BLAST results are now sorted by e-value instead of bitscore. Before the sorting takes place, results from the same query sequence are grouped together. This grouping can make the results appear out of order especially if a low hits per sequence was requested.
    • BLAST Result sorting - The "advanced sort" does not work when evalue is the primary sort field.
    • Exporting large files - exporting large files may result in an error due to memory limitations
    • DB alignments per sequence - user gets error if max of 50,000 is exceeded
    • Megablast errors - Running with the non default parameter, "gapped alignment: false" results in an "error" or "completed with error" status
    • Incorrect program choices (BLAST) - If you upload a protein sequence, the system doesn't properly recognize that it's a protein and offers program choices based on nucleotides. You should cut/paste if the sequence(s) are not too large.
  • Remaining Issues
    • "export matching subjects as fasta" file may contain duplicate values.
    • My FRV Pipeline Jobs - Jobs from v1.3.1 and earlier currently do not load the Fragment Recruitment Viewer properly
    • Recent searches - Keyword searches from v1.3.1 and earlier show up with 0s on the Dashboard
    • Incorrect program choices (BLAST) - If you choose to rerun a old job, and you change to a different type of dataset (Nuc to Prot or Prot to Nuc), it will not run the correct program. The dropdown menu correctly displays the right choices, but the blast results table shows the actual program that the system ran.
  • Please report any problems to camera-help@calit2.net

Database Updates

December 21, 2008

The following 14 datasets were updated in the production database. The * datasets were disabled when v1.3.2 was released

All Prokaryotic Genomes (N)
All Prokaryotic Proteins (P)
CAMERA's Non-Identical Nucleotide Sequences (N) *
CAMERA's Non-Identical Peptide Sequences (P)
Draft Prokaryotic Genomes (N)
Eukaryotic Microbial Genomes (N) *
Eukaryotic Microbial Proteins (P)
Finished Prokaryotic Genomes (N)
Fungal Genomes (N)
Fungal Proteins (P)
MarineMicrobes: Moore Foundation Marine Microbial Genomes (N) *
MarineMicrobes: Moore Foundation Marine Microbial Peptides (P) *
Viral Genomes (N)
Viral Proteins (P)

Production Release (v1.3.2)

November 19, 2008

  • Improvements
    • New Export options for BLAST
    • Improved Export functionality, including new formats and performance improvements
    • Improved Job status page
    • Customized CSV output for different data types
    • Firefox 3 support

  • Fixes
    • Fixed - possible incomplete BLAST result when submitting concurrent jobs using the same query sequence
    • Fixed - BLAST's nongraceful handling of unprintable characters in defline
    • Fixed - external links to NCBI in search details page
    • Fixed - DeepMed 16S fasta not downloadable from proj/pub
    • Fixed - corrupted data in some GOS data downloads
    • Fixed - Incorrect number of matches or results shown in project search

  • Data Updates
    • a substantial update to sequences imported from NCBI/etc (PANDA)
    • additional ORFs and Peptides for the Moore Funded Indian Ocean subset of GOS
    • replaces HOT ORFs/Peptides/ncRNAs with results from improved pipeline
    • new ORFs/Peptides/ncRNAs for:
      AcidMine, Alvinella, CBVIRIO, DeepMed, EBPRSludge, FarmSoil, GutlessWorm,
      MarineBrine, ViralSpring, and Whalefall

  • Known Issues
    • "export matching subjects as fasta" file may contain duplicate values.
    • BLAST Result sorting - In this release, the BLAST results are now sorted by e-value instead of bitscore. Before the sorting takes place, results from the same query sequence are grouped together. This grouping can make the results appear out of order especially if a low hits per sequence was requested.
    • BLAST Result sorting - The "advanced sort" does not work when evalue is the primary sort field.
    • My FRV Pipeline Jobs - Jobs from v1.3.1 and earlier currently do not load the Fragment Recruitment Viewer properly
    • Recent searches - Keyword searches from v1.3.1 and earlier show up with 0s on the Dashboard
    • Exporting large files - exporting large files may result in an error due to memory limitations
    • DB alignments per sequence - user gets error if max of 50,000 is exceeded
    • Megablast errors - Running with the non default parameter, "gapped alignment: false" results in an "error" or "completed with error" status
    • Incorrect program choices (BLAST) - If you upload a protein sequence, the system doesn't properly recognize that it's a protein and offers program choices based on nucleotides. You should cut/paste if the sequence(s) are not too large.
    • Please report any problems to camera-help@calit2.net