A major effort was directed toward establishing, improving, and maintaining linkages and interfaces on the main index page of the Analytical Biostatistics Section (ABS) website implemented on the absalpha server.A series of programs which analyze ligand experiments, dose-response curves, and time series data were added to the webpage as downloadable, executable routines (both PC and Macintosh versions); these include LIGAND, ALLFIT, FLEXFIT, and PULSEFIT. Documentation including publications were added using a scanner and Adobe Acrobat. A facility to keep track of users in a registration log was appended.Interfaces between various protein sequence algorithms were developed, for example the REPORT utility which converts secondary protein structure predictions of several algorithms to a general format called FASTA and also a 'pretty' converter which takes lists of characters in FASTA format and puts them into the 'pretty' format. A design modification to these utilities was added to allow data from file input as well as text box input and in either HTML or plain text format. This design modification was also added to several protein sequence algorithms. The FORTRAN program called by the QL algorithms required a major rewrite to debug it.A conversion from the output of the basic local alignment tool (BLAST) to FASTA format had not worked for some time. The overlying C program failed to call the underlying FORTRAN program; this was repaired and error checking was added. The same problem in sending BLAST output to QL was fixed in the same way.A secondary structure predictor called SIMPA was put up on the ABS page and an interface developed to modify output from an alignment program (CLUSTALW) to be a compatible input for SIMPA.A tool called, """"""""HTML Coffee Cup Editor"""""""" was downloaded into the local PC and tested. This tool automates many of the more difficult things to achieve with HTML.Future Plans: All the work on the ABS webpage will be transferred from the absalpha server to a new Hewlett-Packard machine. Until transfer is complete, all programs on absalpha must be maintained. After transfer all programs will need to be verified and validated.
| Holbrook, P G; Geetha, V; Beaven, M A et al. (1999) Recognizing the pleckstrin homology domain fold in mammalian phospholipase D using hidden Markov models. FEBS Lett 448:269-72 |
| Di Francesco, V; Munson, P J; Garnier, J (1999) FORESST: fold recognition from secondary structure predictions of proteins. Bioinformatics 15:131-40 |
| Geetha, V; Di Francesco, V; Garnier, J et al. (1999) Comparing protein sequence-based and predicted secondary structure-based methods for identification of remote homologs. Protein Eng 12:527-34 |
