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Use Database | Auto-Annotate Sequence to annotate prokaryotic genomes
Read more: Use Database | Auto-Annotate Sequence to annotate prokaryotic genomesThe continuing advances in Next Generation Sequencing have made it relatively low cost to sequence prokaryotic genomes. Many scientists are embarking on large projects to sequence multiple related genomes. These might be clinical isolates of the same species exhibiting different pathogenetic properties, environmental isolates from different sites, or a study over time of the changes…
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Which DNA Matrix to use in Align To Folder?
Read more: Which DNA Matrix to use in Align To Folder?The Database | Align To Folder function is a very useful tool to find and retrieve similar sequences from folders on your computer or on other local machines. Think of it as your own personal BLAST service. It can not only search individual sequences in any format MacVector can read (MacVector, Genbank, EMBL, ABI etc)…
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Gap closing and genome finishing tools in Align to Reference and Assembler.
Read more: Gap closing and genome finishing tools in Align to Reference and Assembler.Automated algorithms can only take you so far with genome assembly. The final steps involved in finishing a genome always need manual intervention. MacVector’s various assembly editors have many tools for helping finish genome sequencing projects. For example, closing gaps, extending reference sequences and even automatically circularizing contigs. If you select reads, then right click…
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MacVector 17 Workshop at The Crick
Read more: MacVector 17 Workshop at The CrickRoom: HR Training Room 01–2162. Floor: 1 Date: 15 October 2019 From: 9:30 to 11:30 Now rescheduled – Date to be advised Chris Lindley of MacVector, Inc. will be giving a training workshop for both novice and advanced users of MacVector at The Crick, reviewing both basic and advanced functions. In particular new tools introduced over the…
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Migrating your Vector NTI sequence database to MacVector.
Read more: Migrating your Vector NTI sequence database to MacVector.ThermoFisher (owners of Invitrogen) have announced that Vector NTI Express is nearing the end of its life and Vector NTI Advanced was terminated quite some time ago. If you are looking for an easy to use sequence analysis application, then look for a reliable and trusted application. MacVector is easy to use, has a comprehensive…
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Identifying transposon insertion sites from multiplexed NGS data
Read more: Identifying transposon insertion sites from multiplexed NGS dataTransposon mutagenesis is a common approach for investigating gene function in bacterial genomes by selecting for clones where the transposon inserting into the genome has generated a specific phenotype. You can then simply sequence the entire genome of each clone by NGS to identify the transposon insertion site. To lower the cost of such experiments,…
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Human Transcriptome RNA-Seq Analysis Using MacVector
Read more: Human Transcriptome RNA-Seq Analysis Using MacVectorWith MacVector Pro and Assembler you can use Bowtie to perform RNA-Seq analyses using NGS data. The interface even has specialized output tabs listing the coverage information and statistics for each annotated CDS and gene feature on the genome. You can download a short tutorial and a sample dataset that illustrate the analysis workflow using…
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Use a right-click in the Editor tab to see if your contig can be circularized
Read more: Use a right-click in the Editor tab to see if your contig can be circularizedMacVector incorporates no less than THREE different de novo assemblers, phrap, velvet and SPAdes. While all are great assemblers, with each having their own specific advantages, none of them will generate a circular sequence from input reads. However, MacVector also includes a tool to help you with this. If you are assembling reads representing plasmid…
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Import Multi-Sequence Genbank Files into an Assembly Project for easy access to Features
Read more: Import Multi-Sequence Genbank Files into an Assembly Project for easy access to FeaturesThere are many genomes in the Genbank database that cannot be downloaded as single annotated sequences. These might be large multi-chromosome eukaryotic genomes, but, increasingly, partially sequenced bacterial chromosomes where the major contigs have been annotated using the NCBI annotation pipeline. Typically, when you encounter these, there are options to download annotated versions of these…
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Opening Genbank or FASTA files with multiple sequences as individual sequences
Read more: Opening Genbank or FASTA files with multiple sequences as individual sequencesMany sequence formats contain multiple concatenated sequence entries. For example FASTA and Genbank are two formats capable of storing multiple individual sequences. By default MacVector will treat such sequences as alignments and open them in the Multiple Sequence Alignment editor. Most users who want to open such a file do want to see an alignment.…
