What's New in MacVector 15.1?
The primary change in MacVector 15.1 is a complete rewrite of the underlying BLAST and Entrez code to conform to the changes in the NCBI server code as required by the US Government. A second NCBI change regarding the deprecation of GI numbers has been addressed at the same time. As always, there are also a number of minor enhancements and bug fixes designed to improve your everyday experience using MacVector. You can view the release notes here.
NCBI Access Via HTTPS:
The US Government has required that all government run web services move to the more secure https: protocol by the end of 2016. The NCBI announced in early summer that they would enable HTTPS access to their services in September 2016 and would turn off all of the old HTTP services before the end of the year. In the caee of the Entrez and BLAST services used by versions of of MacVector prior to 15.1, these will be unavailable from Dec 1st 2016 onwards. MacVector 15.1 has been rewritten to use the new https: services and will be unaffected by these cahnges.
NCBI GI Changes
Historically, the NCBI have identified sequences by both an accession number (e.g. NC_001387) and a "GI Number", e.g. "9507346". If a sequence was modified after submission to GenBank, the accession number would remain the same, but the GI number would change. This led to some complicated situations, so the NCBI are proposing to stop assigning GI numbers, but instead to use Accession.Version numbers to identify sequences. So the example above would have an accession number of NC_001387.1. If the entry was updated and the sequence changed, the new accession number would become NC_001387.2. MacVector 15.1 handles all these changes seamlessly, ensuring you always have access to the latest version of a sequence, whilst still allowing you to look at earlier versions by searching for the appropriate accession.version number.
MacVector now recognizes gzipped (.gz) Fasta and Fastq files, so there is no need to decompress these before using in Bowtie, Velvet or Align To Folder analyses.
Velvet now allows KMER values up to 299, allowing better assembly of MiSeq data and other sources of reads over ~150 nt in length. If you are assembling MiSeq NGS data, try starting with KMER values in the 220 to 270 range for best results.
The Align To Reference SNPs tab no longer calculates the data for each read if more than 20,000 reads are present in an alignment. This lets you align large NGS data sets to a long reference sequence and not have to wait many hours for the individual Read SNP data to be calculated. However, you can still view a list of SNPs in the consensus.