![]() ![]() Positions where one sample has an insert result in a Variance Table row with a gap listed in the Reference Sequence’s column. All of the maps draw correctly now no matter how many millions of bases are being represented. ĭisplay of Restriction Sites, Features, Motifs and Start/Stop Codonsĭepending on the size of the sequence and the window, there were certain situations when Restriction maps, Features and Motifs, and Start/Stop maps would display incorrectly, truncating or even wrapping in the middle.This performance improvement is most noticeable in calculating and displaying the Overview (including features, motifs, and codon map), the Restriction Map and Sequence inset map elements. Performance Improvements for Large Sequences and Contigs Working with sequences and contigs millions of bases long is now up to hundreds of times faster.Hardware requirements depend upon your project’s needs but at minimum should be 512MB RAM and 175MB hard disk space. Sequencher 5.0 Requirements: Mac OS X 10.5 or 10.6, Windows XP or later. ![]() Select a range of bases or 1 or more sequences and contigs in your project and choose the Sequence > NCBI Blast Search command. The search mode is designed for quickly checking regions of your data. We’ve added the ability to perform Blast searches from within Sequencher. To view the Methylation tolerant alignment results, choose the Sequence > Analyses > GSNAP Methylation Analysis command. The Ts will have been converted by the bisulfite treatment prior to sequencing and, therefore, were unmethylated. GSNAP performs a mismatch tolerant alignment that allows Cs in the reference sequence to match Ts in the sequencing reads. To view the SNP-tolerant alignment results, choose the Sequence > Analyses > GSNAP SNP Analysis command. GSNAP reports back on the found known SNPs and any new mismatches. You provide the reference sequence, reads and a list of known SNPs. You may perform a SNP-tolerant alignment with GSNAP. To open the report, choose the Sequence > Analyses > Maq SNP Report command. Maq allows you to search for SNPs using a two stage filtering process, the results of which are presented in a report. Regardless of whether you choose to view the aligned reads immediately, the consensus results aligned to the Reference Sequence will be added to your current project allowing you to view the contig later in the appropriate viewer by selecting the consensus sequence or contig in your project and choosing the Contig > Show NGS Data Using command. ![]() You may immediately view the NGS alignment results in Maqview‡ or Tablet§ viewers after alignment with Maq or GSNAP has completed. There is a new Assemble menu that consolidates the commands for the NGS alignment algorithms with Sequencher’s existing Assemble Contigs commands that were previously on the Contig menu. To perform an alignment with either algorithm, select a single sequence in your project and choose the Assemble > Align Data Files to Ref Using command. You can choose where these files are saved by setting the Gene Codes Home Directory on the new External Data User Preference pane. These data results may often be very large files.
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