Tag: entrez
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Searching and downloading sequences from Entrez
MacVector has integrated connectivity to the NCBI BLAST and Entrez databases. You can directly search Entrez for DNA or Protein sequences based on features, authors, keywords etc and directly download them into MacVector, complete with all features and annotations.
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How to change the default appearance of features
If you download a sequence from Entrez, or open a sequence that is not in MacVector format, MacVector assigns a default appearance to any features on the sequence. For example, CDS features are shown as a blue arrow with a Helvetica 9 point font label. With the advent of ultra high resolution displays, you may…
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Download the latest published version of your favorite sequence with its accession number
It’s very quick to download the latest version of a sequence if you know its accession number. When you start working with a new sequence, it’s the best place to start. Go to DATABASE > ENTREZ Enter the accession number of your favorite sequence Click SEARCH Double click on the result to open up your…
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Viewing external database entries for features in a sequence.
Sequences, or regions of sequences, can be linked to external databases. For example an entire sequence entry or for when annotation tools are used to annotate proteins with domain or motif information (e.g. InterProScan available in MacVector 15). Very useful for when you want to view more detailed or updated information. Within the Genbank specification,…
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IMPORTANT SERVICE ANNOUNCEMENT Entrez and BLAST services will stop working in November for MacVector 15.0.3 and earlier.
UPDATE – November 8, 2016 – Although the official switch off date is not until Wednesday the 9th, Entrez and BLAST are NOT currently working from MacVector 15.0.3 and earlier. We suspect this change is now permanent. UPDATE – November 7, 2016 – We have just been notified by the NCBI that they will be…
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Download the latest published version of your favorite sequence with its accession number
It’s very quick to download the latest version of a sequence if you know its accession number. When you start working with a new sequence, it’s the best place to start. Go to DATABASE > ENTREZ Enter the accession number of your favorite sequence Click SEARCH Double click on the result to open up your…
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The oldest entries in Genbank? Some fun for Labor day.
Inspired by some tweets from @ewanbirney, because I’m waiting for lunch and because it’s Labor Day I used the Entrez tool to find the oldest entries (using the publication date field) in Genbank. For proteins there’s a single hit in 1979 For NA there’s 12 hits from 1982: Nothing useful here and it’s probably not…