Manually-performed sequences are usually human-read from X-ray films. This is especially employed for clone fingerprinting (A-tracks), where results are analysed by the TRACKS program, developed in house. Automatic sequencers, such as Li-Cor, perform the data acquision automatically.
Sequence assembly
Sequences are assembled using BAP or GAP (Dear & Staden, 1991) and custom-made command line interfaces.
Sequence analysis
Sequence analysis is performed on SUN workstations using software developed by the OGMP Informatics Division and others such as the Staden sequence analysis package. The FASTA program (Pearson, 1990) is used for searches of local databases; sequence similarity searches are also performed at the National Center for Biotechnology Information (NCBI), using the BLAST network service (Altschul et al., 1990). The CLUSTALV and W (Higgins & Sharp, 1989) and PIMA (Smith & Smith, 1992) programs are used for multiple protein alignments. Analysis is commonly managed from the GDE package (Genetic Data Environment; Smith et al, 1994). BLAST searches are conducted with the batch utility BBLAST and results inspected with TBOB (Text Blast Output Browser). Phylogenetic analysis is performed using the PHYLIP package as well as custom tools such as PARBOOT.
A number of other programs, including multiple sequence file manipulation, pre-processing, and conversion utilities for XBAP, FASTA and GDE, have been developed in the Informatic Division of the OGMP's Sequencing Unit and are available through the Internet.
Return to the OGMP molecular methods page.