Month: March 2019

Run the Prokaryotic Genome Annotation Pipeline (PGAP) on your own machine

You can now download PGAP from GitHub and run it on your machine, compute farm or the cloud, on any public or privately-owned genome. PGAP predicts genes on bacterial and archaeal genomes using the same inputs and applications used inside NCBI. This is a great opportunity for you to try it now and send us comments (please use GitHub issues).

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MANE Select v0.5 is now available!

In October last year, we announced the launch of an exciting new collaboration between NCBI and EMBL-EBI called MANE (Matched Annotation from the NCBI and EMBL-EBI). As a first step, we began generating the MANE Select set, comprising a matched representative transcript for every human protein-coding gene. Now that our genome resources are integrated into a high-quality transcript set, you don’t need to choose between RefSeq and Ensembl/GENCODE datasets for genomic analyses.

Not only does the MANE Select set make it easier for you to exchange data or translate coordinates between RefSeq and Ensembl annotation results, but you’ll also be able to use the set with NGS-based sequencing technologies and other resources that use the latest and highest-quality reference human genome assembly available.

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IgBLAST 1.13.0 now available

IgBLAST is a popular NCBI package for classifying and analyzing  immunoglobulin and T cell receptor variable domain sequences. We’ve released a new version of IgBLAST with three new improvements:

  1. The new release determines the V gene reading frame from the end of FWR3 region instead of end of V gene.  This helps identify the correct reading frames for rearrangements that have insertions or deletions near the V gene end.
  2. The allowed distance between V gene end and J gene start has been increased to 225 bp to allow detection of ultra long D/N regions.
  3. The standalone program and files has been repackaged to make it easier  to install.

The new release is available from the BLAST FTP area, along with a new manual on GitHub.

Improved search makes it easier to find antimicrobial resistance protein information

It’s now easier to find known antimicrobial resistance (AMR) protein information at NCBI. You can search by gene symbol, protein name, or accession across NCBI databases and retrieve the best representative DNA sequence that is a reference for antimicrobial resistance genes from the National Database of Antibiotic Resistant Organisms (NDARO).

AMR_allele

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Track pathogenic organisms promptly with the National Database of Antibiotic Resistant Organisms

In response to the rising threat of antimicrobial resistance (AMR), NCBI built the National Database of Antibiotic Resistant Organisms (NDARO). With NDARO, you can:

FIG 1
Figure 1. Filter your Isolates Browser results based on date, location, and for antibiotic resistance (whether the isolate has any AMR genes, or any Antimicrobial Susceptibility Testing (AST) phenotype submitted).

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Change the way your graphs look with Genome Data Viewer’s enhanced settings

If you need to change your graph type – say, from histogram to line graph or a heat map – in Genome Data Viewer (GDV), you can now do so with a few clicks.

Click on the track name of any graph track to change the display (see Figure 1A, B and C).

Fig1
Figure 1. Click on a track name to expose the graph settings menu (A). Set graph display style (B) to histogram, heat map or line graph (C).

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