From jeedward from yahoo.com Wed Feb 6 10:37:18 2008 From: jeedward from yahoo.com (John Edward) Date: Wed Feb 6 10:37:34 2008 Subject: [Genbank-bb] Draft paper submission deadline is extended: BCBGC-08 Message-ID: <564921.81433.qm@web45906.mail.sp1.yahoo.com> Dear Professors, Colleagues and Friends Kindly share the announcement below with those who may be interested: thank you in advance. Sincerely John Edward BCBGC-08 Draft paper submission deadline is extended. The 2008 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) (website: www.PromoteResearch.org ) will be held during July 7-10 2008 in Orlando, FL, USA. The draft paper submission deadline is extended until February 19 2008 due to several requests from the authors. The conference will be held at the same time and location where several major events (see below) will be taking place. BCBGC brings together both academic and industrial scientists and developers from a diverse range of disciplines including bioinformatics, computer science, computational biology, genomics, proteomics and chemoinformatics. One of the main goals of the conference is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers in different fields. Papers that demonstrate applications of existing techniques or developments of new methods are equally welcomed to the conference. Sincerely John Edward ? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-08) ? International Conference on Automation, Robotics and Control Systems (ARCS-08) ? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-08) ? International Conference on Enterprise Information Systems and Web Technologies (EISWT-08) ? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-08) ? International Conference on Software Engineering Theory and Practice (SETP-08) ? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-08) --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/genbankb/attachments/20080206/e77ee161/attachment.html From cavanaug from ncbi.nlm.nih.gov Thu Feb 14 11:56:36 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Thu Feb 14 11:56:47 2008 Subject: [Genbank-bb] GenBank 164.0 Close-of-Data Message-ID: <7F40ACD22B0A23448C4E8755E5875FE71004BBED@NIHCESMLBX8.nih.gov> Greetings GenBank Users, Close-of-data for the upcoming GenBank Release 164.0 occurred on Tuesday February 12 at approximately 1:30am EST. The subsequently generated GenBank Incremental Update files nc0212.aso, nc0212,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 164.0 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 Feb 15 12:34:02 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Fri Feb 15 12:34:12 2008 Subject: [Genbank-bb] Protein FASTA files for GenBank releases : new location and file convention Message-ID: <7F40ACD22B0A23448C4E8755E5875FE7101B2448@NIHCESMLBX8.nih.gov> Prior to February 2008, a FASTA product for protein sequences from coding regions annotated on the DNA sequences in GenBank has been provided as a single large file: ftp://ftp.ncbi.nih.gov/genbank/relNNN.fsa_aa.gz where 'NNN' represents a 3-digit GenBank release number. The uncompressed size of this file has grown to exceed 4GB, which is unmanageable for many users. So as of GenBank Release 164.0, individual protein FASTA files will be provided on a per-division basis, in a new subdirectory of the NCBI FTP site: ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta One such file would be named: gbpri1.fsa_aa.gz Further information will be available via a README file in the new ncbi-asn1/protein_fasta directory, when the Release 164.0 files are made installed (possibly by Saturday February 16). Note that the location of the protein FASTA files is within the /ncbi-asn1 area, not the /genbank area. Since the protein FASTA files have a 1-to-1 correspondence with NCBI's ASN.1 files, this is a more natural location for them. [In fact, the quality-score data files currently located in /genbank/quality_scores would *also* be located more naturally in the /ncbi-asn1 area. They may be relocated at a future date.] The old single-file protein FASTA product will be supported for two more GenBank releases, through Release 166.0 in June of 2008. But after that release, the relNNN.fsa_aa.gz file will be discontinued. Mark Cavanaugh GenBank NCBI/NLM/NIH/HHS From cavanaug from ncbi.nlm.nih.gov Tue Feb 19 01:17:39 2008 From: cavanaug from ncbi.nlm.nih.gov (Cavanaugh, Mark (NIH/NLM/NCBI) [E]) Date: Tue Feb 19 01:17:48 2008 Subject: [Genbank-bb] GenBank Release 164.0 Now Aailable Message-ID: <7F40ACD22B0A23448C4E8755E5875FE70CAF5645@NIHCESMLBX8.nih.gov> Greetings GenBank Users, GenBank Release 164.0 is now available via FTP from the National Center for Biotechnology Information (NCBI): Ftp Site Directory Contents ---------------- --------- --------------------------------------- ftp.ncbi.nih.gov genbank GenBank Release 164.0 flatfiles ncbi-asn1 ASN.1 data used to create Release 164.0 Close-of-data for GenBank 164.0 occured on 02/12/2008. Uncompressed, the Release 164.0 flatfiles require roughly 321 GB (sequence files only) or 342 GB (including the 'short directory', 'index' and the *.txt files). The ASN.1 data require approximately 295 GB. Recent statistics for non-WGS, non-CON sequences: Release Date Base Pairs Entries 163 Dec 2007 83874179730 80388382 164 Feb 2008 85759586764 82853685 Recent statistics for WGS sequences: Release Date Base Pairs Entries 163 Dec 2007 106505691578 26177471 164 Feb 2008 108635736141 27439206 During the 56 days between the close dates for GenBank Releases 163.0 and 164.0, the non-WGS/non-CON portion of GenBank grew by 1,885,407,034 basepairs and by 2,465,303 sequence records. During that same period, 1,750,703 records were updated. An average of about 75,286 non-WGS/non-CON records were added and/or updated per day. Between releases 163.0 and 164.0, the WGS component of GenBank grew by 2,130,044,563 basepairs and by 1,261,735 sequence 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 164.0 and Upcoming Changes) have been appended below. ** Important Notes ** A new GenBank division will become legal as of Release 165.0 in April 2008: the Transcriptome Shotgun Assembly, or TSA, division. Please see Section 1.4.1 of the release notes for more information about TSA and the records that it will contain. 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 164.0 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: February 15 2008, 164.0). 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 164.0, 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 164.0 1.3.1 Organizational changes The total number of sequence data files increased by 10 with this release: - the CON division is now comprised of 85 files (+1) - the ENV division is now comprised of 8 files (+1) - the HTC division is now comprised of 13 files (+1) - the EST division is now comprised of 694 files (+19) - the GSS division is now comprised of 277 files (-18) (see Note below) - the HTG division is now comprised of 107 files (+2) - the INV division is now comprised of 12 files (+1) - the PAT division is now comprised of 35 files (+1) - the PLN division is now comprised of 28 files (+1) - the PRI division is now comprised of 35 files (+1) The total number of index files increased by 2 with this release: - the AUT (AUTHOR Name) index is now comprised of 50 files (+2) NOTE: A configuration setting that determines the average size for many of the GSS division GenBank flatfiles was mistakenly changed for Release 163.0. This resulted in a filesize decrease for a large number of GSS flatfiles, from 230 MB to 210 MB. Consequently, the total number of GSS flatfiles underwent an artificially-large increase of 26 files. The configuration setting was restored for GenBank Release 164.0. As as a result, there is now an apparent net decrease of 18 GSS files. Our apologies for any confusion that this may have caused. 1.3.2 Divisional protein FASTA files now available Individual protein FASTA data files are now being made available for GenBank releases, in the ASN.1 area of the NCBI FTP site: ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta Each protein FASTA file reflects the protein data content of the ASN.1 data file bearing the same division code in its name. For example, these two "pri12" divisional files: gbpri12.aso.gz gbpri12.fsa_aa.gz are 'equivalent', in that the proteins annotated on the DNA sequences of gbpri12.aso are all present in gbpri12.fsa_aa.gz . For further information, please see this README: ftp://ftp.ncbi.nih.gov/ncbi-asn1/protein_fasta/README.protein_fasta These divisional files are a replacement (see Section 1.4.2) for the single protein FASTA file that has been provided in conjunction with GenBank releases: ftp://ftp.ncbi.nih.gov/genbank/relNNN.fsa_aa.gz where 'NNN' represents a three-digit GenBank release number. 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-one of the GSS flatfiles in Release 164.0. Consider gbgss227.seq : GBGSS1.SEQ Genetic Sequence Data Bank February 15 2008 NCBI-GenBank Flat File Release 164.0 GSS Sequences (Part 1) 86927 loci, 64285938 bases, from 86927 reported sequences Here, the filename and part number in the header is "1", though the file has been renamed as "227" 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 New GenBank TSA division: Transcriptome Shotgun Assembly A new GenBank division for assembled mRNA sequences, Transcriptome Shotgun Assembly (TSA), will be included in GenBank releases on or after Release 165.0 in April of 2008. 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" will be present for 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. TSA records make use of the same PRIMARY block that is utilized for Third-Party Annotation (TPA) records. The PRIMARY block will contain references to the underlying reads/transcripts that were assembled to construct the 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. 1.4.2 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