From cavanaug from ncbi.nlm.nih.gov Thu Jun 12 10:51:59 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Thu Jun 12 10:52:14 2008 Subject: [Genbank-bb] GenBank 166.0 Close-of-Data Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC013BF009@NIHCESMLBX15.nih.gov> Greetings GenBank Users, Close-of-data for the upcoming GenBank Release 166.0 occurred on Wednesday June 11 at approximately 1:30am ET. The subsequently generated GenBank Incremental Update files nc0611.aso, nc0611,flat, etc. contain data through the close. Note: Release processing often does not begin until sometime during business hours on the close date. As a result, a number of sequence records processed *after* 1:30am are likely to be present in the GenBank 166.0 release files, even though they are "post-close" . Similarly, the first GenBank Incremental Update that is generated after the close date is likely to contain a number of sequence records that are unchanged, compared to their appearance in the release files. Our apologies for the lack of advanced notice about the close date. Mark Cavanaugh GenBank NCBI/NLM/NIH/HHS From cavanaug from ncbi.nlm.nih.gov Fri Jun 13 21:51:40 2008 From: cavanaug from ncbi.nlm.nih.gov (Mark Cavanaugh) Date: Fri Jun 13 21:51:49 2008 Subject: [Genbank-bb] GenBank Release 166.0 Now Available Message-ID: <4853323C.mailO541ZY3FR@widget0.be-md.ncbi.nlm.nih.gov> A non-text attachment was scrubbed... Name: not available Type: application/octet-stream Size: 9879 bytes Desc: not available Url : http://www.bio.net/bionet/mm/genbankb/attachments/20080613/7acd567d/attachment.exe From cavanaug from ncbi.nlm.nih.gov Fri Jun 13 22:03:16 2008 From: cavanaug from ncbi.nlm.nih.gov (Mark Cavanaugh) Date: Fri Jun 13 22:03:25 2008 Subject: [Genbank-bb] GenBank Release 166.0 Now Available Message-ID: <200806140303.m5E33GY1013529@goliath.ncbi.nlm.nih.gov> [Apologies for the double-post : The contents of my original post about Release 166.0 availability will be interpreted as an attachment under some circumstances...] Greetings GenBank Users, GenBank Release 166.0 is now available via FTP from the National Center for Biotechnology Information (NCBI): Ftp Site Directory Contents ---------------- --------- --------------------------------------- ftp.ncbi.nih.gov genbank GenBank Release 166.0 flatfiles ncbi-asn1 ASN.1 data used to create Release 166.0 Close-of-data for GenBank 166.0 occured on 06/11/2008. Uncompressed, the Release 166.0 flatfiles require roughly 343 GB (sequence files only) or 366 GB (including the 'short directory', 'index' and the *.txt files). The ASN.1 data require approximately 314 GB. Recent statistics for non-WGS, non-CON sequences: Release Date Base Pairs Entries 165 Apr 2008 89172350468 85500730 166 Jun 2008 92008611867 88554578 Recent statistics for WGS sequences: Release Date Base Pairs Entries 165 Apr 2008 110500961400 26931049 166 Jun 2008 113639291344 39163548 During the 57 days between the close dates for GenBank Releases 165.0 and 166.0, the non-WGS/non-CON portion of GenBank grew by 2,836,261,399 basepairs and by 3,053,848 sequence records. During that same period, 376,881 records were updated. An average of about 60,188 non-WGS/non-CON records were added and/or updated per day. Between releases 165.0 and 166.0, the WGS component of GenBank grew by 3,138,329,944 basepairs and by 12,232,499 records. GenBank has surpassed the 200-billion basepair threshold, with a total of 205,647,903,211 bases as of this June 2008 release. For additional release information, see the README files in either of the directories mentioned above, and the release notes (gbrel.txt) in the genbank directory. Sections 1.3 and 1.4 of the release notes (Changes in Release 166.0 and Upcoming Changes) have been appended below. ** Important Notes ** * A new GenBank division appears with Release 166.0 : the Transcriptome Shotgun Assembly, or TSA, division. Please see Section 1.3.2 of the release notes for more information about TSA and the records that it contains. * Support for the single, comprehensive protein FASTA file which accompanies GenBank releases ceases with this June 2008 release. See Section 1.4.1 of the release notes for details. * GenBank 'index' files are now provided without any EST content, and without most GSS content. See Section 1.3.3 of the release notes for further details. NCBI is considering ceasing support for the index files, so we encourage affected users to review that section and provide feedback. Release 166.0 data, and subsequent updates, are available now via NCBI's Entrez and Blast services. As a general guideline, we suggest first transferring the GenBank release notes (gbrel.txt) whenever a release is being obtained. Check to make sure that the date and release number in the header of the release notes are current (eg: June 15 2008, 166.0). If they are not, interrupt the remaining transfers and then request assistance from the NCBI Service Desk. A comprehensive check of the headers of all release files after your transfers are complete is also suggested. Here's how one might go about this on a unix platform, using csh/tcsh : set files = `ls gb*.*` foreach i ($files) head -10 $i | grep Release end Or, if the files are compressed, perhaps: gzcat $i | head -10 | grep Release If you encounter problems while ftp'ing or uncompressing Release 166.0, please send email outlining your difficulties to: info@ncbi.nlm.nih.gov Mark Cavanaugh, Vladimir Alekseyev, Michael Kimelman GenBank NCBI/NLM/NIH/HHS 1.3 Important Changes in Release 166.0 1.3.1 Organizational changes The total number of sequence data files increased by 47 with this release: - the TSA division is now comprised of 1 file (+1) - the BCT division is now comprised of 29 files (+1) - the CON division is now comprised of 91 files (+6) - the EST division is now comprised of 738 files (+25) - the ENV division is now comprised of 9 files (+1) - the GSS division is now comprised of 290 files (+5) - the HTG division is now comprised of 117 files (+3) - the PAT division is now comprised of 42 files (+4) - the PRI division is now comprised of 36 files (+1) The total number of index files increased by 4 with this release: - the AUT index is now comprised of 54 files (+4) 1.3.2 New file for the Transcriptome Shotgun Assembly (TSA) division As announced with the previous release, Release 166.0 contains a new divisional file (gbtsa.seq) for Transcriptome Shotgun Assembly (TSA) mRNA sequences. TSA sequences are shotgun assemblies of primary sequences deposited in dbEST, the Trace Archive (TA) or the Short-Read Archive (SRA). Keywords "TSA" and "Transcriptome Shotgun Assembly" are present on all TSA records, in addition to a division code value of "TSA" on the LOCUS line. No format changes (new or changed line types, features, or qualifiers) are anticipated for this new class of GenBank record. However, note that TSA records make use of the same PRIMARY block that is utilized for Third-Party Annotation (TPA) records. The PRIMARY block contains references to the underlying reads/transcripts that were assembled to construct a TSA record. It might be helpful to review the content of TSA record EZ000001 and its use of the PRIMARY block: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=189498984 Requirements for the new Transcriptome Shotgun Assembly division include: 1. Submission of primary transcipt sequence data to dbEST, the Trace Archive, or the Short-Read archive (SRA). 2. Registration of an associated transcriptome project with the International Nucleotide Sequence Database Collaboration (INSDC). For information about submitting projects via NCBI/GenBank, see: http://www.ncbi.nlm.nih.gov/genomes/mpfsubmission.cgi 3. Submission of TSA sequence records to GenBank, including an assembly file (.ace format) Note that TSA records and the primary transcript sequences that they are built from must be provided by the same submitter or collaborative group. 1.3.3 Changes in the content of index files As described in the GB 153 release notes, the 'index' files which accompany GenBank releases (see Section 3.3) are considered to be a legacy data product by NCBI, generated mostly for historical reasons. FTP statistics of January 2005 seem to support this: the index files were transferred only half as frequently as the files of sequence records. The inherent inefficiencies of the index file format also lead us to suspect that they have little serious use by the user community, particularly for EST and GSS records. The software that generated the index file products received little attention over the years, and finally reached its limitations in February 2006 (Release 152.0). The required multi-server queries which obtained and sorted many millions of rows of terms from several different databases simply outgrew the capacity of the hardware used for GenBank Release generation. Our short-term solution is to cease generating some index-file content for all EST sequence records, and for GSS sequence records that originate via direct submission to NCBI. The three gbacc*.idx index files continue to reflect the entirety of the release, including all EST and GSS records, however the file contents are unsorted. These 'solutions' are really just stop-gaps, and we will likely pursue one of two options: a) Cease support of the 'index' file products altogether. b) Provide new products that present some of the most useful data from the legacy 'index' files, and cease support for other types of index data. If you are a user of the 'index' files associated with GenBank releases, we encourage you to make your wishes known, either via the GenBank newsgroup, or via email to NCBI's Service Desk: info@ncbi.nlm.nih.gov Our apologies for any inconvenience that these changes may cause. 1.3.4 GSS File Header Problem GSS sequences at GenBank are maintained in two different systems, depending on their origin, and the dumps from those systems occur in parallel. Because the second dump (for example) has no prior knowledge of exactly how many GSS files will be dumped by the first, it does not know how to number its own output files. There is thus a discrepancy between the filenames and file headers for fifty-nine of the GSS flatfiles in Release 166.0. Consider gbgss232.seq : GBGSS1.SEQ Genetic Sequence Data Bank June 15 2008 NCBI-GenBank Flat File Release 166.0 GSS Sequences (Part 1) 87182 loci, 64465152 bases, from 87182 reported sequences Here, the filename and part number in the header is "1", though the file has been renamed as "232" based on the number of files dumped from the other system. We will work to resolve this discrepancy in future releases, but the priority is certainly much lower than many other tasks. 1.4 Upcoming Changes 1.4.1 Comprehensive protein FASTA file to be discontinued Given the availability of divisional protein FASTA files as of GenBank Release 164.0, support for the single, large, comprehensive protein FASTA file: ftp://ftp.ncbi.nih.gov/genbank/relNNN.fsa_aa.gz (where 'NNN' represents a three-digit GenBank release number) will be discontinued after GenBank Release 166.0 in June of 2008. The size of this file has grown to exceed 4GB, which is unmanageable for many users. Users are advised to make plans to utilize the new divisional files by August of 2008. The divisional protein FASTA files are located at: ftp://ftp.ncbi.nih.gov/ncbi-asn1/gbXXX.fsa_aa.gz From francis from oicr.on.ca Sat Jun 14 10:19:14 2008 From: francis from oicr.on.ca (Francis Ouellette) Date: Sat Jun 14 12:13:44 2008 Subject: [Genbank-bb] GenBank Release 166.0 Now Available In-Reply-To: <200806140303.m5E33GY1013529@goliath.ncbi.nlm.nih.gov> Message-ID: > From: Mark Cavanaugh > > GenBank has surpassed the 200-billion basepair threshold, with a total > of 205,647,903,211 bases as of this June 2008 release. Wow 200 billion nucleotides! I remember when we celebrated 1 Billion nucleotides! Good work all the folks at the NCBI - good way to celebrate 25 years! Cheers, f. -- B.F. Francis Ouellette http://oicr.on.ca/research/ouellette/ We are hiring a "Manager, Web Development": http://tinyurl.com/4dgyuk NextGen sequencing Bioinformatics Workshop: http://tinyurl.com/29ulqj