Berkeley DB XML is a native XML database engine for use within your product. Made available as a C++ library with language bindings for Java, Perl, Python, PHP, and Tcl, it integrates directly into your application (it is not a standalone database server). It provides XQuery access into a database of document containers. XML documents are stored and indexed in their native format using Berkeley DB as the transactional database engine.
The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems. It is not trying to be the last word in informatics benchmarking, as there are simply too many codes, tests, data sets, and databases. The goal is to create a core of tests that all may download and use to probe specific elements of system performance. The end goal is to enable a pluggable set of tests, including the core tests, so that performance data may be gathered.
ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. It is not a gene prediction program, nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity.
MuGeN is a package for interactively exploring multiple annotated genomes simultaneously, possibly mixed with computational analysis results. Map information can be loaded from various sources, and resulting images can be exported in different formats. Both an interactive GUI based environment and a batch mode program are provided.
PDBCat can be used to manipulate and process PDB files using commonly available text-processing tools such as Perl, awk, etc. The Brookhaven Protein Data Bank stores atomic coordinate information for protein structures in a column-based format which is designed to be read easily read by FORTRAN programs. PDBCat converts the ATOM and HETATM records of PDB files from this column-based format to a field-based one that is more easily processed by standard Unix tools.
PerlPrimer is a GUI application that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR), and sequencing. It aims to automate and simplify the process of primer design. Current features include calculation of possible primer-dimers, retrieval of genomic or CDNA sequences from Ensembl (including both sequences automatically for QPCR), the ability to BLAST search primers using the NCBI server, ORF, and CpG island detection algorithms, the ability to add cloning sequences to primers, automatically adjusted to be in-frame, and QPCR primer design without manual intron-exon boundary entry.