New plug-ins and plug-in updates

• MLST module updated
  • Possible to download MLST schemes from any web site compatible with mlstDBnet
  • When a new allele is called because the sequencing reads are not long enough, this is reported in the isolate view rather than "New allele"

See a list of all plug-ins here.

New and improved features

• Multi-site Gateway Cloning. You can perform multi-site gateway cloning and in a few clicks create your expression clones with multiple fragments. The existing Gateway Cloning tool has been expanded so that you can easily recombine several fragments as well as continue using it for the standard Gateway Cloning.
• Process tagged sequences
  • A summary report is now available with an overview of the number of reads per bar code.
  • You can search for barcodes (MIDs) on both strands, supporting new 454 protocol.
• Find Binding Sites and Create Fragments improved:
  • If your template sequence contains ambiguity nucleotides (like N, Y etc), these will no longer count as mismatches when checking your primers. Note that the primer base of course need to be covered by the ambiguity symbol (e.g. a T would still be a mismatch if the template sequence has an R, which means either A or G).
  • Fixed: When using multiple template sequences, the choices to open or annotate a fragment from the fragment table did not work properly. They always applied to the first sequence although the fragment was located on another sequence (as indicated in the table).
• Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.

Bug fixes

• Fixed: Annotations spanning the sequence from start to end did not display right when the sequence was wrapped. The annotation was only displayed on the first line.
• Fixed: Set-up experiment would crash when using many samples.
• Fixed: Calculation of consensus sequence in read mappings: Sometimes a majority of gaps would be ignored and a base erroneously introduced in the consensus sequence. It occurs when 1) there is no coverage in an initial segment of the reference sequence, and 2) a gap is encountered in the global read alignment. From that point onwards, gap counts are included in the consensus vote, but they are taken from the start of the mapping (where they are all 0), so they are out of sync with associated base counts. High gap counts would then kick in further downstream, possibly making the consensus a gap where it should not be. We recommend checking your mapping results manually if you rely on using the consensus sequence for further analysis.
• Fixed: importing adapters for trimming and barcodes for de-multiplexing did not work properly for CSV files and empty rows in Excel files were not allowed.
• Fixed: Motif search did not exclude regions with Ns when the option "Exclude matches in N-regions for simple motifs" was selected.

New plug-ins and plug-in updates

• MLST module updated
  • Possible to download MLST schemes from any web site compatible with mlstDBnet
  • When a new allele is called because the sequencing reads are not long enough, this is reported in the isolate view rather than "New more...