From cavanaug from ncbi.nlm.nih.gov Tue Aug 25 12:32:47 2009 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Tue Aug 25 15:45:58 2009 Subject: [Genbank-bb] GenBank 173.0 Close-Of-Data Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC07F2D842@NIHCESMLBX15.nih.gov> Greetings GenBank Users, Close-of-data for the upcoming GenBank Release 173.0 occurred on Friday August 21 2009 at approximately 1:30am EDT. The subsequently generated GenBank Incremental Update files nc0821.aso, nc0821.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 173.0 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. We expect to make the GenBank 173.0 data files available sometime tomorrow. Our apologies for the lack of advanced notice about the close date, and for delays that have affected the delivery of the GB 173 product. Mark Cavanaugh GenBank NCBI/NLM/NIH/HHS From cavanaug from ncbi.nlm.nih.gov Wed Aug 26 21:24:45 2009 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Wed Aug 26 21:48:18 2009 Subject: [Genbank-bb] GenBank Release 173.0 Now Available Message-ID: <7B6F170840CA6C4DA63EE0C8A7BB43EC03EF92FD@NIHCESMLBX15.nih.gov> Greetings GenBank Users, GenBank Release 173.0 is now available via FTP from the National Center for Biotechnology Information (NCBI): Ftp Site Directory Contents ---------------- --------- --------------------------------------- ftp.ncbi.nih.gov genbank GenBank Release 173.0 flatfiles ncbi-asn1 ASN.1 data used to create Release 173.0 Close-of-data for GenBank 173.0 occured on 08/21/2009. Uncompressed, the Release 173.0 flatfiles require roughly 408 GB (sequence files only) or 437 GB (including the 'short directory', 'index' and the *.txt files). The ASN.1 data require approximately 370 GB. Recent statistics for non-WGS, non-CON sequences: Release Date Base Pairs Entries 172 Jun 2009 105277306080 106073709 173 Aug 2009 106533156756 108431692 Recent statistics for WGS sequences: Release Date Base Pairs Entries 172 Jun 2009 145959997864 49063546 173 Aug 2009 148165117763 48443067 During the 72 days between the close dates for GenBank Releases 172.0 and 173.0, the non-WGS/non-CON portion of GenBank grew by 1,255,850,676 basepairs and by 2,357,983 sequence records. During that same period, 654,396 records were updated. An average of about 41,838 non-WGS/non-CON records were added and/or updated per day. Between releases 172.0 and 173.0, the WGS component of GenBank grew by 2,205,119,899 basepairs, while the number of sequence records decreased by 620,479 (due to some WGS projects being re-assembled into fewer, but larger, records). 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 173.0 and Upcoming Changes) have been appended below for your convenience. ** Important Notes ** * GenBank 'index' files are now provided without any EST content, and without most GSS content. See Section 1.3.5 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 173.0 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: August 15 2009, 173.0). 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 173.0, please send email outlining your difficulties to: info@ncbi.nlm.nih.gov Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky, Sergey Zhdanov GenBank NCBI/NLM/NIH/HHS 1.3 Important Changes in Release 173.0 1.3.1 Organizational changes The total number of sequence data files increased by 28 with this release: - the BCT division is now composed of 48 files (+3) - the ENV division is now composed of 17 files (+1) - the EST division is now composed of 886 files (+11) - the GSS division is now composed of 340 files (+3) - the HTC division is now composed of 15 files (+1) - the HTG division is now composed of 134 files (+1) - the PAT division is now composed of 79 files (+6) - the PLN division is now composed of 38 files (-1) - the PRI division is now composed of 40 files (+1) - the TSA division is now composed of 2 files (+1) - the VRT division is now composed of 19 files (+1) Note: The decline in the number of PLN division files is due to the fact that twelve records representing the chromosomes of Oryza sativa Japonica Group have been converted to a CON-division representation. See section 1.3.2 for more details. The total number of 'index' files increased by 1 with this release: - the AUT (author) index is now composed of 66 files (+1) 1.3.2 Twelve Oryza sativa Japonica Group records moved to CON division. Prior to Release 173.0, the sequence records for 12 Oryza sativa Japonica Group chromosomes had been 'traditional' records, totalling over 382 Mbp of sequence data. However, on August 7 2009, the records were converted to a CON-division representation, with CONTIG-line join() statements that describe how the chromosomes are constructed from underlying PAC and fosmid sequences. The records involved are: LOCUS AP008207 45064769 bp DNA linear CON 07-AUG-2009 LOCUS AP008208 36823111 bp DNA linear CON 07-AUG-2009 LOCUS AP008209 37257345 bp DNA linear CON 07-AUG-2009 LOCUS AP008210 35863200 bp DNA linear CON 07-AUG-2009 LOCUS AP008211 30039014 bp DNA linear CON 07-AUG-2009 LOCUS AP008212 32124789 bp DNA linear CON 07-AUG-2009 LOCUS AP008213 30357780 bp DNA linear CON 07-AUG-2009 LOCUS AP008214 28530027 bp DNA linear CON 07-AUG-2009 LOCUS AP008215 23843360 bp DNA linear CON 07-AUG-2009 LOCUS AP008216 23661561 bp DNA linear CON 07-AUG-2009 LOCUS AP008217 30828668 bp DNA linear CON 07-AUG-2009 LOCUS AP008218 27757321 bp DNA linear CON 07-AUG-2009 Due to this change, these chromosomal records are now present in file gbcon1.seq of the CON division. In addition, the total number of Oryza sativa Japonica Group basepairs listed in the table in Section 2.2.7 has declined by 370,461,808 bases, compared to Release 172.0. The table intentionally excludes CON-division records, to avoid double-counting of underlying sequence records and any larger-scale objects that are constructed from them. 1.3.3 File header problem for EST and GSS files A new method of generating the EST and GSS sequence files has been developed, which has reduced the time required to generate a GenBank release by one day. However, a minor problem in the formatting of the header of the sequence files was inadvertently introduced : a leading space exists before the filename on the very first line. For example: GBGSS100.SEQ Genetic Sequence Data Bank August 15 2009 It should be: GBGSS100.SEQ Genetic Sequence Data Bank August 15 2009 The problem effects all EST files and most GSS files. We had hoped to repair this formatting issue for Release 173.0, but the code changes which were expected to fix the problem did not perform correctly. It is hoped that this issue will be resolved for Release 174.0 . 1.3.4 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. 1.3.5 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 seventy-two of the GSS flatfiles in Release 173.0. Consider gbgss269.seq : GBGSS1.SEQ Genetic Sequence Data Bank August 15 2009 NCBI-GenBank Flat File Release 173.0 GSS Sequences (Part 1) 87186 loci, 64231458 bases, from 87186 reported sequences Here, the filename and part number in the header is "1", though the file has been renamed as "269" based on the number of files dumped from the other system. We hope to resolve this discrepancy at some point, but the priority is certainly much lower than many other tasks. 1.4 Upcoming Changes 1.4.1 New class of /exception value As of October 2009, a new class of /exception will be available for use on coding region features: /exception="annotated by transcript or proteomic data" This exception will be used for situations in which: the protein sequence (presented via the coding region's /translation qualifier) differs from the conceptual translation; the quality of the DNA sequencing is high; and there is evidence at the transcript or proteome level that the presented protein *is* actually expressed by the organism. An inference qualifier of type "similar to" should be used in conjunction with this new type of exception, to indicate the supporting EST/cDNA/protein sequence. An updated definition of /exception, with examples for this new type of exception value, will be provided via the GenBank newsgroup prior to the October release. 1.4.2 /haplogroup qualifier introduced A haplotype is a combination of alleles at multiple loci that are transmitted together on the same chromosome. A haplogroup is a group of similar haplotypes that share a common ancestor with a single nucleotide polymorphism mutation. The majority of submitters of complete human mitochondrial genomes provide information about their haplogroup rather than their haplotype. Stable mtDNA polymorphic variants clustered together in specific combination form a haplogroup. To accomodate this need, a new /haplogroup qualifier will be introduced as of GenBank Release 174.0 in October 2009. A formal definition of /haplogroup was not available as of the creation of these release notes, so it will be provided via the GenBank newsgroup prior to the October release. 1.4.3 /artificial_location qualifier introduced A new qualifier, intended for use in limited genome-scale annotation contexts, will be introduced as of GenBank Release 175.0 in December 2009: Qualifier /artificial_location Definition indicates that location of the CDS or mRNA is modified to adjust for the presence of a frameshift or internal stop codon and not because of biological processing between the regions. This is expected to be used only for genome-scale annotation, either because a heterogeneous population was sequenced, or because the feature is in a region of low-quality sequence. 1.4.4 /pseudo qualifier renamed as /non_functional Because the term "pseudo" is often assumed to mean "pseudogene", the /pseudo qualifier will be renamed as /non_functional, to better reflect its actual usage in the sequence databases. This change will take place as of the April 2010 GenBank Release.