Bioinformatics has now become an inseparable part of modern biology. With the advent of high-end computers, statistical analysis now provides a strong support for scientific research. As a result, there arises a need for user-friendly software that can provide all of the necessary bioinformatics tools. I use Vector NTI (Invitrogen), which contains virtually all of the most commonly used bioinformatics tools (such as alignment, BLAST, PubMed, citation viewer, 3D molecule viewer, etc.). The software comes with a database that has information on a large number of protein molecules, plasmid maps, restriction enzymes, gel markers, etc.
I frequently use the tool for drawing vector maps. It can make high-resolution maps and display all of the commonly used restriction enzyme sites. The database provided contains vector maps for most plasmids and they can be used as templates to make other plasmid maps. Restriction enzymes can be added to the database and existing ones can be edited. Drawing a new map is very simple and both sequence- and non-sequence maps can be drawn. In sequence maps, you can search for the restriction sites easily. Maps can be copied to the clipboard and pasted to power point slides or MS word. The drawn figures are scaled to the number of base pairs specified. Inserted fragments can be colored differently. Site-directed mutagenesis can be performed in silico and it can also design the most suitable primers for DNA amplification, as well as, for sequencing. The contig viewer can be used to align contigs of sequenced genomes.
Protein sequences available in the database can be edited or updated using any online database. Sequence retrieval can be performed using BLAST and can be performed with either the entire protein sequence or just a portion. The query results can be downloaded, saved and viewed later. It has tools for both pairwise and multiple alignments, as well as, back-translation of amino acid sequences and theoretical digestion of proteins with different proteases. A 3D molecule viewer is provided for rendering .pdb files. Pubmed citations can also be searched and downloaded using this software.
The software takes little hard-drive space, however adding more information to the database may require more room. Processor use is high, especially while performing multiple sequence alignments and it is better to run this software on platforms with a reasonably good configuration. It consumes a good amount of both RAM and system virtual memory. A network connection is required for web-based searches.
All the results generated from different tools can be easily copied and pasted to MS Word or PowerPoint without alteration of formatting. First-time users are strongly encouraged to read the manual for setting up optimal search and filtering criteria, especially if they do not possess sufficient bioinformatics knowledge.
Vikas Jain
Research Scholar
Indian Institute of Science
India