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2000
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May 3
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- The pairwise alignment program, LFASTA was off.
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May 1
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- Three new programs for Drosophila Genome search have been added to the Search Launcher, BLASTN, BLASTP and TBLASTN.
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Mar. 30
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- Upgraded web server to Apache 1.3.12.
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Mar. 23
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- New URL of Search Launcher:
The BCM Search Launcher has been given a new, easy to remember URL: http://searchlauncher.bcm.tmc.edu /. The old URL http://searchlauncher.bcm.tmc.edu / is still accessible.
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Mar. 14
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- Updated the Annotated Domains Database used with BEAUTY
and BEAUTY-X
searches. Annotations included are from Entrez database version 116, PRINTS version 25, PROSITE version 16, BLOCKS release 11, PFAM version 5.0, Domo release 2.0, and Prodom release 2000.1.
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Feb. 25
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- A new program, Sequence Chopover has been added to the Sequence Utilities page. It cuts a large protein/DNA sequence into smaller ones with certain amounts of overlap.
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Feb. 15
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- A new feature has been added to the Six Frame Translation. From the Options page, you can select specific frames for translation. The default is all the six frames.
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Feb. 2
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- A link to the Protein Data Bank has been added to the BEAUTY_BLASTP and BEAUTY_BLASTX searches. This link provides a way to predict a tertiary structure from an unknown peptide (particularly if it is incomplete) after searching for sequence similiarity using BEAUTY searches.
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Jan. 2
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- The web server software has been upgraded to Apache 1.3.9.
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1999
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Dec. 28
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- Updated the Annotated Domains Database used with BEAUTY
and BEAUTY-X
searches. Annotations are included from Entrez database version 114, PRINTS version 24, PROSITE version 15, BLOCKS release 11, and PFAM version 4.3. Two new annotation databases are added to this Annotated Domains Databse, Domo release 2.0, and Prodom release 99.2.
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Dec. 14
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-Clustalw, Multiple Sequence Alignment has been upgraded to version 1.8
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Nov. 22
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-New version of Search Launcher Batch Client has been released.
Win32-search-launcher2.7.pl for DOS and Search-launcher-2.7.pl for Unix.
This new version is especially helpful to Win95/NT users. With our previous version, the whole search list, about 100 searches, are displayed immediately after starting the Batch Client. DOS/NT users can not see the instructions at all. With this new release, it will display about 15 searches each time.
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Sept 29
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-As the users' request, a new feature is added to the sixframe translation on page Sequence Utilities.
-Our search tool BLASTX 1.4 + BEAUTY on page Nucleic Acid Search is removed, since BLAST 1.4 is retired from NCBI.
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Sept 3
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-The Annotated Domain Database on which BEAUTY relies is updated.
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June 8
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- Implemented PBS queuing software for WU-BEAUTYX 2.0 searches (available on the nucleic acids search page).
- Began updating the user during the for WU-BEAUTYX 2.0 searches (available on the nucleic acids search page). This will allow the user to both know what is actually happening and also to let us know where any problems might be. Future plans include the addition of the queue status to the update pages.
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June 2
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- Began updating the user during the for BEAUTYX 1.4 searches (available on the nucleic acids search page). This will allow the user to both know what is actually happening and also to let us know where any problems might be. Future plans include the addition of the queue status to the update pages.
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June 1
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- Implemented PBS queuing software for BEAUTYX 1.4 searches (available on the nucleic acids search page). This software, when fully implemented for all searches, will allow us to maximize the use of our server and allow faster turn-around time for searches. We expect to complete the implementation of PBS into all of our searches by the end of summer 1999.
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May 5
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- Updated PhD to use the Predict Protein server at Columbia University. Predict protein is a service for sequence analysis and structure prediction. Predict protein can be found on the protein secondary structure prediction page.
- Added BOXSHADE link and instructions to PIMA (Pattern Induced (local) Multiple Alignment) program output. BOXSHADE is a program for pretty-printing multiple alignment output. It can output files in a number of formats including ASCII, postscript (PS) and encapsulated postscript (EPS), rich-text environment (RTF). PIMA performs a multi-sequence alignment of a set of (presumably related) sequences using an extension of the covering pattern construction algorithm of Smith and Smith 1990 (Abstract) and 1992 (Abstract). PIMA can be found on the multiple sequence alignment page.
- Added BOXSHADE link and instructions to MAP program output. BOXSHADE is a program for pretty-printing multiple alignment output. It can output files in a number of formats including ASCII, postscript (PS) and encapsulated postscript (EPS), rich-text environment (RTF). MAP can be found on the multiple sequence alignment page.
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May 3
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- Added the High Throughput Genomic Sequence database to the nucleic acids search page.
- Added BOXSHADE link and instructions to ClustalW program output. BOXSHADE is a program for pretty-printing multiple alignment output. It can output files in a number of formats including ASCII, postscript (PS) and encapsulated postscript (EPS), rich-text environment (RTF). ClustalW can be found on the multiple sequence alignment page.
- Added BCM human genomic sequence database to the BLAST options page.
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April 28
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- Added microbial genomes to the nucleic acids search page.
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April 21
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- Upgraded server software to Apache 1.3.6.
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April 19
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- Added the BCM Human Transcript Database to the nucleic acids search page. The Human Transcript Database (HTDB) is a curated source for information related to RNA molecules that have been sequenced. The goal of the HTDB is to provide a clone-based platform that represents as any of the human transcripts that have been sequenced as possible. As the focus of the HTDB is on complete or nearly complete sequences, EST sequence information has been excluded.
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March 20
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- Switched to a higher speed computer system that has 4 processors and 1 GB RAM. All URIs will remain the same.
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March 19
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- Updated the Annotated Domains Database used with BEAUTY
and BEAUTY-X
searches. Annotations are included from Entrez database entries up to Feb 1999, PRINTS version 22, PROSITE version 15, and BLOCKS release 12. This updated database contains 269,121 protein sequences.
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March 1
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- The BCM Search Laucher has moved its home page to http://www.hgsc.bcm.tmc.edu/SearchLauncher/. This change was made because the Human Genome Sequencing Center moved its website to http://www.hgsc.bcm.tmc.edu/.
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1998
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- Added Cognitor searches of the COG database to the
protein search page.
Cognitor provides a sequence similarity search of the Clusters of Orthologous Groups (COGs) database. The COGs database is built from protein sequences found in completely sequenced genomes. Each COG represents a conserved protein family.
- Added tRNAscan-SE to the
Nucleic Acid Sequence Search Page . tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes,
with a false positive rate of less than one per 15 gigabases.
- Added the Searches of the Toxoplasma database of clustered ESTs from University of Pennsylvania to the
Nucleic Acid Sequence Search Page .
- Version 2.6 of the Search Launcher Batch Client for Macintosh released.
- Server upgraded to Apache 1.3
- WU-BLASTP was updated to version 2.0 and BEAUTY output was added
- Added BEAUTY output to FASTA searches.
- BLASTP is now run locally instead of through NCBI
- - Added several new genome databases and their appropriate tools to the Species-Specific Protein Search Page. Most of these queries are sent to other servers after being checked. The new
additions include:
- a) TBLASTN version 1.4 through the OU server is available to
search the genomes of Actinobacillus actinomycetemcomitans, Aspergillus nidulans,
Neurospora crassa, Cryptococcus neoformans, Neisseria gonorrhoeae, Staphylococcus aureus,
Streptococcus pyogenes, and Streptococcus mutans
- b) TBLASTN version 1.4 through TIGR, is available to
search the end sequences of BAC and P1 clones of Trypanosoma brucei.
- c) WU-BLASTP and WU-TBLASTN through Stanford is available to search the Arabidopsis genome.
- d) WU-TBLASTN through Sanger Sanger is available to search the
genomes of Campylobacter jejune, Mycobacterium leprae, Neisseria meningitidis, Streptomyces
coelicolor, Mycobacterium tuberculosi, S. pombe, and Yersinia pestis. WU-BLASTP is also
available for Mycobacterium tuberculosis and S. pombe.
- e) FASTA, through the TIGR server is available to search the
genomes of Treponema pallidum and Helicobacter pylori (this genome can also be searched
with TFASTA).
- Added Contig Assembly Program (CAP) to the multiple sequence alignment page.
- Added BLASTN search of the dbsts database to the Nucleic Acid Sequence Search page.
- Added BLASTN search of the est_mouse database to the Nucleic Acid Sequence Search page.
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- Added several species specific searches:
- BLASTN / Actinobacillus actinomycetemcomitans genome - BLASTN 1.4 (OU)
- BLASTN / Fungal (Aspergillus nidulans and Neurospora crassa) genomes - BLASTN 1.4 (OU)
- BLASTN / B. subtilis - BLAST2 search of B. subtilis strain 168 (Pasteur)
- WU-BLASTN / C. elegans genomic - 6-frame translation vs. genomic (Sanger)
- WU-BLASTX / C. elegans wormpep - 6-frame translation vs. wormpep (Sanger)
- WU-TBLASTX / C. elegans EST - 6-frame translation vs. translated C. elegans EST (Sanger)
- BLASTN / Cryptococcus neoformans genome - BLASTN 1.4 (OU)
- BLASTN / Neisseria gonorrhoeae genome - BLASTN 1.4 (OU)
- WU-BLASTN / S.cerevisiae Genome - Warren Gish's BLAST with gapped
alignments (Stanford SGD)
- WU-BLASTN / S. pombe genome - Warren Gish's BLAST with gapped
alignments (Sanger)
- BLASTN / Staphylococcus aureus genome - BLASTN 1.4 (OU)
- BLASTN / Streptococcus pyogenes genome - BLASTN 1.4 (OU)
- BLASTN / Streptococcus mutans genome - BLASTN 1.4 (OU)
- BLASTN / Synechocystis sp. strain PCC 6803 Genome - (CyanoBase)
- WU-BLASTN / ToxoDB - WU-BLASTN search of the Toxoplasma database of clustered
ESTs (UPENN)
- BLASTN / Trypanosoma brucei genome - BLASTN 1.4 search ofTrypanosoma brucei BAC and
P1 End (TIGR)
- BLASTX is now run locally instead of through NCBI
- Species specific searches are now available on the web instead of only email as in the past.
- Added BLAST2 to the pairwise sequence alignment page.
- Added LAP2 to the pairwise sequence alignment page.
- Added PGWISE and PCWISE to the pairwise sequence alignment page.
- Added SOUSI to the Protein Secondary Structure Prediction page.
- Added Protein Hydrophilicity/Hydrophobicity Search to the Protein Secondary Structure Prediction page.
- Added RepeatMasker to the Sequence Utilities page.
- Added e-PCR (PCR based STS detection).
- Released version 2.5 of the BCM Search Launcher Batch Client for Unix, PC and Mac.
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