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into a single portal interface, with direct pointers to the relevant information at the collections’ websites, providing both historical traces and geographical distribution of the strains they keep in culture. In addition, the information for Pseudomonas species and/or strains is automatically linked to related sequences in the public domain and refers to existing scientific publications that deal with the organism. Figure 1 General overview of the process for maintenance, queries, and analysis of gene sequences using the PseudoMLSA Database server http://www.uib.es/microbiologiaBD/Welcome.html. The isolate,
strain or Pseudomonas species information can be easily queried by searching against several fields. Furthermore, users can BIX 1294 datasheet do sequence-based Wnt inhibitor searches against database including user’s own sequence datasets. Advanced Bay 11-7085 searches are possible via configurable BLAST parameters. A more fine-tuned clustering analysis can be carried out with programs included in the PHYLIP package. Since the alignment of nucleotide
or amino acid sequences is one of the most important tools for researchers involved in gene sequence comparison for identification purposes, users can also upload their own sequence datasets to query against. The basic local alignment search tool (BLAST), which predominates as the fastest and most widely-used tool, has been included as a web-based interface to search against the PseudoMLSA sequence database. The BLAST program is widely used for sequence similarity searches [32] because it provides an easy way for a user to perform BLAST searches via a web server, and it suits the general purpose of searches against the curated PseudoMLSA database. Additionally, a web interface for PHYLIP programs [26, 33] is implemented to carry out more precise evolutionary studies. The PseudoMLSA database offers an interface for choosing between a user-definable set of target databases, and inputting user uploaded query sequences by pasting them directly into the query box, or by uploading sequences as FASTA files from a local computer. Users can also manipulate the BLAST parameters to glean more specific information.