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Customizing BLAST alignment results to make mismatches more noticeable
Read more: Customizing BLAST alignment results to make mismatches more noticeableWhen you run a Blast search, as well as a list of hits, you will get a list of alignments between your query sequence and each hit. As with most other text alignments in MacVector, identical matches are by default represented by a vertical line (a score greater than 1) and mismatches (whether similar or…
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How to save contig consensus sequences from assembly projects
Read more: How to save contig consensus sequences from assembly projectsThe MacVector Assembler module lets you create projects, populate them with Sanger Sequencing or NGS data files (or any sequences in a format that MacVector can read) and then assemble them using the popular phrap and/or Velvet assemblers. Typically, the result will be a collection of contigs that you might want to use in additional…
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Search fastq files and retrieve matching reads into paired fastq files
Read more: Search fastq files and retrieve matching reads into paired fastq filesThe Database | Align To Folder… function is essentially your own personal BLAST search of sequences on your computer, but with the advantage that you can scan fasta/fastq containing millions of entries and retrieve matching Reads into a new file. MacVector 14.5 added an enhancement where you can search paired-end read files and retrieve both…
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How to retrieve BLAST hits from the Aligned Sequences result tab
Read more: How to retrieve BLAST hits from the Aligned Sequences result tabAfter a BLAST search, you can retrieve matching sequences from the Description List results tab. What you may not know is that you can do a similar thing from the Aligned Sequences result tab. One advantage of this approach is that (as in the example above) sometimes there are multiple accession numbers for a hit.…
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Displaying CDS features as translations in the Map tab.
Read more: Displaying CDS features as translations in the Map tab.MacVector uses CDS features extensively in many areas. If you know the coding region, then it’s very useful to have that annotated to your sequence. For example you can display a CDS feature as its translation directly under the sequence in the Editor tab. You can also display the translation of a feature in the…
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Screening for CRISPR Indels using Align To Reference
Read more: Screening for CRISPR Indels using Align To ReferenceMacVector’s Analyze | Align To Reference… tool is ideal for screening reads for the short insertions, deletions or substitutions resulting from CRISPR experiments. Simply open your reference sequence, choose Analyze | Align To Reference…, click on the Add Seqs toolbar button to add reads from different clones/experiments, then click on Align to align the reads…
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How to align DNA sequences based on their amino acid translations
Read more: How to align DNA sequences based on their amino acid translationsA new tool in MacVector 15 allows you to align DNA sequences based on their amino acid translated sequence. For most alignments in MacVector you will use the Multiple Sequence Alignment tool. This allows you to align DNA or protein sequences using either Muscle, Clustalw or T-Coffee. MacVector 15 now allows you to align DNA…
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Functional domain analysis of protein sequences using InterProScan
Read more: Functional domain analysis of protein sequences using InterProScanThere’s a new tool in MacVector 15 that allows you to do functional domain analysis on your protein sequence using the InterProScan service. InterPro contains multiple databases of protein families, domains and motifs and InterProScan will submit a protein sequence to a search of these databases. It will also do extra analysis such as transmembrane…
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Create your own Primer Database.nsub from an Excel spreadsheet
Read more: Create your own Primer Database.nsub from an Excel spreadsheetWouldn’t it be great if there was an easy way of converting that huge primer collection you have into a format that MacVector can use? Well, luckily there is! There is a utility called “Primer Converter” that you can download from our website. To use the utility you first need to get your primers into…
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Use Analyze->Primer Database Search to scan sequences for primer binding sites
Read more: Use Analyze->Primer Database Search to scan sequences for primer binding sitesIt’s easy to keep track of all your primers using a MacVector subsequence (.nsub) file. We even ship MacVector with a starter file called “Primer Database.nsub” that you can find in the /Applications/MacVector/Subsequences/ folder. If you choose Analyze | Primer Database Search… and use this default file to search pUC19, you’ll find many of the…
