14 November, 2003: More expression data from NASCArrays has been added for each gene on the Affymetrix ATH1 chip, find the results within protein families on the AMPL Mainpage. A description of the new data is here, including a key. You can search for expression data for any gene on the ATH1 chip using the search engine on the left menu.
14 April, 2003: Expression data from NASCArrays has been added for each gene on the Affymetrix ATH1 chip, find the results within protein families on the AMPL Mainpage. A description of the data is here, including a key. 4 October 2002 - New version of AMPL uses ATH1 data release 3.0 from TIGR dated
2 August 02. Details on the data release from Chris Town are available here. Now 10569 gene models are supported by full-length cDNA sequences. In addition, links to TAIR were added for each sequence.
4 October 2002 - Homologs from human have now been added and can be found under the "Relatives" link for each protein family along with links to homologous sequences in rice, yeast, Drosophila, and C. elegans. You can access the human, rice, yeast, C. elegans, and Drosophila membrane protein libraries directly through this link.
2 August 2002 - New version of AMPL uses predicted protein sequence available from TIGR in January 2002. Links to homologous sequences in rice, yeast, Drosophila, C. elegans can be found for each family under the Relatives link. You can access the yeast, C. elegans, and Drosophila membrane protein libraries directly through this link.
19 July 2002 - new version of AMPL based on predicted protein sequence available from TIGR in Jan. 2002. In this version, links to homologous sequences in rice can be found for each protein family under "Relatives". The new Rice Membrane Protein Library is located here. Links from Arabidopsis to yeast, C. elegans, and Drosophila homologs are not currently available but will be added. You can access the yeast, C. elegans, and Drosophila membrane protein libraries directly through this link.
5 Aug, 2001 - Identification of homologous sequences in yeast, C. elegans, and Drosophila was added under the "Relatives" link for each family.
1 Aug, 2001 - New link on the left menu for families of unknown function that have "relatives" in Arabidopsis.
13 July, 2001 - A new "relatives" link was added to each protein family that shows additional homologous sequences in Arabidopsis. This will be useful if you are trying to compile a complete family tree. Check out the "relatives" link in your favorite family.
10 June, 2001 - AMPL upgraded with protein sequence file from TIGR dated March 20, 2001. A keyword search has been added - it is useful to identify the family containing a particular AGI code (Atxgxxx number), to identify all families within a superfamily (i.e. search using MFS, ABC or AAAP) or to find all families with a specific function (i..e. search on calcium).
19 April, 2001 - The Yeast Membrane Protein Library (YMPL) is a genome-wide analysis of Saccharomyces cerevisiae generated using the software tools developed for AMPL. In YMPL, all proteins with two or more predicted membrane spanning domains are clustered into families by sequence holomolgy. Alignments and FastA files for each family are available for download as well as a single FastA file with the 1593 membrane protein sequences and other results from the analysis.
13 March, 2001- Transporter View was added, a page dedicated to information on all transporters identified in Arabidopsis.
23 February, 2001- Links were added to Milton Saier's site, describing transporter families for the 889 Arabidopsis transporters that have been classified so far by Ian Paulsen.
11 February, 2001- The alignment and matrix generating program bl64.c has been modified to account for comparisons of short sequences with long sequences. The details are here. Links to MIPS were added for the Atxgxxxx accession numbers and other links to public databases were improved. Links are now available (on the left side menu) to other plant membrane protein sites. If you want your site added, send me an email. Finally, with each sequence, TMS domains predicted by HMMTOP are now highlighted in blue.
24 January, 2001- AMPL gets a major upgrade with a current dataset from January 15, 2001. Transmembrane spanning domain prediction is now greatly improved due to the contribution of HMMTOP by Dr. Gabor E. Tusnady. Redundancy is much less now that we are using the publication release data from TIGR. And since the alignment program is running faster we included all proteins with two or more transmembrane spanning domains.
20 November, 2000- After discussion with Christophe Maurel, we decided to move a small family of four sequences that was listed on the "Aquaporins" page. If you are looking for the small family it is now listed at the top of the "Unknown Function" page.
6 November, 2000 - Some optimization was done on the alignment program bl64.c. Thanks to Urs Hochstrasser for stopping by and helping with the revision. The alignment results are the same, but the program runs much faster.
2 November, 2000 - Added links to NCBI for each sequence. Amino acid numbers were n+1 for each sequence and this was corrected.
1 November, 2000 - Family names in the enzymes for cell wall biosynthesis category were updated.
27 October, 2000 - Calcium pump family names changed.
26 October, 2000 - AMPL on line, dataset from Oct. 15, 2000.