From cavanaug from ncbi.nlm.nih.gov Thu Apr 17 13:51:18 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Thu Apr 17 13:51:47 2008 Subject: [Genbank-bb] GenBank 165.0 Close-of-Data Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC990C84@NIHCESMLBX15.nih.gov> Greetings GenBank Users, Close-of-data for the upcoming GenBank Release 165.0 occurred on Monday April 14 at approximately 8:00pm EDT. The subsequently generated GenBank Incremental Update files nc0415.aso, nc0415,flat, etc. contain data through the close. 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 Apr 18 15:52:46 2008 From: cavanaug from ncbi.nlm.nih.gov (Mark Cavanaugh) Date: Fri Apr 18 15:52:55 2008 Subject: [Genbank-bb] GenBank Release 165.0 Now Aailable Message-ID: <200804182052.m3IKqkmM027730@hyperion.ncbi.nlm.nih.gov> Greetings GenBank Users, GenBank Release 165.0 is now available via FTP from the National Center for Biotechnology Information (NCBI): Ftp Site Directory Contents ---------------- --------- --------------------------------------- ftp.ncbi.nih.gov genbank GenBank Release 165.0 flatfiles ncbi-asn1 ASN.1 data used to create Release 165.0 Close-of-data for GenBank 165.0 occured on 04/15/2008. Uncompressed, the Release 165.0 flatfiles require roughly 332 GB (sequence files only) or 353 GB (including the 'short directory', 'index' and the *.txt files). The ASN.1 data require approximately 305 GB. Recent statistics for non-WGS, non-CON sequences: Release Date Base Pairs Entries 164 Feb 2008 85759586764 82853685 165 Apr 2008 89172350468 85500730 Recent statistics for WGS sequences: Release Date Base Pairs Entries 164 Feb 2008 108635736141 27439206 165 Apr 2008 110500961400 26931049 During the 62 days between the close dates for GenBank Releases 164.0 and 165.0, the non-WGS/non-CON portion of GenBank grew by 3,412,763,704 basepairs and by 2,647,045 sequence records. During that same period, 1,590,201 records were updated. An average of about 68,340 non-WGS/non-CON records were added and/or updated per day. Between releases 164.0 and 165.0, the WGS component of GenBank grew by 1,865,225,259 basepairs. The number of records decreased by 508,157 due to the re-assembly of WGS project AAKN, into far fewer (but larger) contigs. 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 165.0 and Upcoming Changes) have been appended below. ** Important Notes ** * A new GenBank division has become legal with this April's Release 165.0 : 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 will contain. * Support for the single, comprehensive protein FASTA file which accompanies GenBank releases will be ceased as of the 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 165.0 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: April 15 2008, 165.0). 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 165.0, 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 165.0 1.3.1 Organizational changes The total number of sequence data files increased by 41 with this release: - the BCT division is now comprised of 28 files (+2) - the EST division is now comprised of 713 files (+19) - the GSS division is now comprised of 285 files (+8) - the HTG division is now comprised of 114 files (+7) - the PAT division is now comprised of 38 files (+3) - the PLN division is now comprised of 29 files (+1) - the VRL division is now comprised of 9 files (+1) 1.3.2 New Transcriptome Shotgun Assembly (TSA) division now legal A new GenBank division for assembled mRNA sequences, Transcriptome Shotgun Assembly (TSA), can now appear in GenBank releases, as of this April 2008 Release 165.0. The date of first appearance of a TSA record will depend on the status of TSA submission processing, but it *is* expected that they will begin to appear in the GenBank Incremental Updates (GIU) within the next month, and that Release 166.0 will include a divisional TSA file. Files in this new division will have filenames of: gbtsaNN.aso.gz (ASN.1 format) gbtsaNN.seq.gz (GenBank flatfile format) where 'NN' represents an integer file-number within the TSA division. 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 Third Party Annotation record BK005658, which provides a good example of PRIMARY block usage: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=83843278 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. Examples of TSA records and more information about how to submit them will be provided in future editions of these release notes, and via the GenBank newsgroup. 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-four of the GSS flatfiles in Release 165.0. Consider gbgss232.seq : GBGSS1.SEQ Genetic Sequence Data Bank April 15 2008 NCBI-GenBank Flat File Release 165.0 GSS Sequences (Part 1) 87177 loci, 64476488 bases, from 87177 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 With 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. If this timetable poses problems, please let us know at the NCBI Service Desk: info@ncbi.nlm.nih.gov