Monkeypox virus: Complete genome from the current outbreak now available in GenBank

The first complete genome sequence of the current monkeypox virus (MPXV) outbreak (isolate name MPXV_USA_2022_MA001) is now available with accession ON563414 in GenBank, a public database of DNA sequences hosted by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM). Several cases of monkeypox have been identified in geographically widespread … Continue reading Monkeypox virus: Complete genome from the current outbreak now available in GenBank

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RefSeq Release 209 is available

RefSeq release 209 is now available online, from the FTP site and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of November 1, 2021, and contains 296,293,486 records, including 215,655,378 proteins, 41,751,205 RNAs, and sequences from 114,396 organisms. The release is provided in several directories as a complete … Continue reading RefSeq Release 209 is available

NCBI will assign 64-bit numeric GIs by November 15th. Update affected software!

As announced  last month, NCBI will begin assigning larger (64-bit) numeric ‘GIs’ to the remaining sequence types that still receive these identifiers. This change is expected as soon as Nov. 15th, 2021 but could occur earlier if data submission volumes are unexpectedly high. This is a reminder that all organizations and developers using our products should review software for any remaining … Continue reading NCBI will assign 64-bit numeric GIs by November 15th. Update affected software!

NCBI’s GI sequence identifiers will soon exceed 32-bit numbers. Are you and your software ready?

In 2016, NCBI announced that it was curtailing its display of its numeric ‘GI’ in popular sequence data formats such as FASTA and GenBank flatfiles. Due to the continued growth of GenBank, NCBI will soon begin assigning GIs exceeding the signed 32-bit threshold of 2,147,483,647 for those remaining sequence types that still receive these identifiers. The exact date … Continue reading NCBI’s GI sequence identifiers will soon exceed 32-bit numbers. Are you and your software ready?

RefSeq release 201 is public

RefSeq release 201 is accessible online, via FTP and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of July 6, 2020, and contains 246,016,651 records, including 178,304,046 proteins, 32,462,009 RNAs, and sequences … Continue reading

Download high-quality graphics from the NCBI Multiple Sequence Alignment Viewer (MSAV)

You can now download a publication-quality graphic images of  the alignment displayed in the NCBI Multiple Sequence Alignment Viewer (Figure 1). Load sequence alignments into the viewer from BLAST or COBALT results or upload alignment files directly. Once you have … Continue reading

RefSeq release 200 is public

RefSeq release 200 is accessible online, via FTP and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of May 4, 2020, and contains 237,381,664 records, including 171,643,729 proteins, 31,244,247 RNAs, and sequences from … Continue reading

The next RefSeq FTP release number will skip to 200

NCBI’s Reference Sequence (RefSeq) FTP release numbers will increment to 200 for the next release and skip over the numbers 100-199. The current, March 2020 release, is release 99. The next bi-monthly release in May 2020 will be release 200.  … Continue reading

RefSeq Release 99 is public

RefSeq release 99 is accessible online, via FTP and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of March 2, 2020, and contains 231,402,293 records, including 167,278,920 proteins, 29,869,155 RNAs, and … Continue reading

RefSeq Release 99 is public

RefSeq release 99 is accessible online, via FTP and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of March 2, 2020, and contains 231,402,293 records, including 167,278,920 proteins, 29,869,155 RNAs, and … Continue reading