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General Research Use collection streamlines access to patient-level data in dbGaP
In response to many requests from dbGaP users to simplify and streamline the data access request process while respecting patient consent, dbGaP staff have identified “General Research Use” individuals from different studies and created a collection that allows users to access data on these individuals through a single access request.
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NCBI to hold two-day genomics hackathon in January
From January 5th to 7th, NCBI will host a genomics hackathon focusing on advanced bioinformatics analysis of next generation sequencing data. This event is for students, postdocs and investigators already engaged in the use of pipelines for genomic analyses from next generation sequencing data. Working groups of 5-6 individuals will be formed for DNA-Seq/multiomics, RNA-seq, metagenomics and Epigenomics. These groups will build pipelines to analyze large datasets within a cloud infrastructure.
NCBI BioSample includes curated list of over 400 known misidentified and contaminated cell lines
The NCBI BioSample database now includes a curated list of over 400 known misidentified and contaminated cell lines. Scientists should check this list before they start working with a new cell line to see if that cell line is known to be misidentified.
NCBI Eukaryotic Genome Annotation Pipeline breaks record; over 100 organisms annotated this year
The NCBI Eukaryotic Genome Annotation Pipeline has broken a record and completed the annotation of over 100 organisms since the beginning of 2014!
NCBI BankIt webinar on December 17th
On December 17th, NCBI will have a webinar entitled "A Submitter's Guide to GenBank: Using BankIt for Small-Scale Nucleotide Sequence Submissions". This presentation will outline the process of using BankIt, a web-based submission tool at NCBI, to submit sequence data to the GenBank database.
NCBI E-Utilities webinar video now on YouTube
October's webinar, "An Introduction to NCBI's E-Utilities, an NCBI API", is now on YouTube and has been added to the NCBI Webinars playlist.
BLAST URL domain change in effect December 1
As announced previously, BLAST searches sent to the www.ncbi.nlm.nih.gov/blast URL will not function as of December 1, 2014. The officially supported URL domain for BLAST searches at the NCBI is blast.ncbi.nlm.nih.gov. Please update your bookmarks, links, and any scripts or applications.
RefSeq release 68 available on FTP
The comprehensive RefSeq release 68 is now available on the FTP site, with over 66 million records describing 46,968,574 proteins, 9,069,704 RNAs, and sequences from 49,312 distinct NCBI TaxIDs.
dbVar releases 1000 Genomes Phase 3 structural variants
dbVar has released structural variation (SV) data generated by the 1000 Genomes Project Phase 3 as dbVar study estd214. This large dataset contains SV from 2,500 subjects, and comprises nearly 63,000 variant regions and over 6 million calls, including insertions, deletions, copy number variants (CNVs), mobile element insertions, indels (deletion-insertions), and inversions. The data are available on assemblies GRCh37 (submitted) and GRCh38 (remapped). Genotypes are currently available in VCF.
dbVar releases copy number variation (CNV) data from developmental delay study cited in Nature Reviews Genetics
dbVar recently released copy number variation (CNV) data from a study on dosage-sensitive genes (PMID: 25217958) that was highlighted in Nature Reviews Genetics. In the study, CNV analysis was combined with protein-truncating single-nucleotide variation (SNV) and targeted resequencing to identify dosage-sensitive genes causing developmental delay.
BLAST+ 2.2.30 released
A new version (2.2.30) of the stand-alone BLAST executables is now available, bringing several improvements to BLAST+. These improvements include tasks for BLASTX and TBLASTN (blastx-fast and tblastn-fast) that use longer words, as described in Shiryev, Papadopoulos, Schaffer, and Agarwala (2007), as well as support for composition-based statistics in RPS-BLAST. A number of bug fixes, including those for FASTA parsing, are also included.