Genomics Made Easy

Abstract

T his is an era in which molecular biologists can often obtain gene sequences of interest by searching databases rather than by screening libraries of cloned DNA fragments. Thus, instead of wandering around labs with tubes of radioactive probes, scientists are often found at their desks, peering hopefully at their computer screens. As whole genomes find their way into the databases, the probability is ever greater that a sequence of interest is only a BLAST search away. Although the power of the Internet makes enormous amounts of sequence data readily accessible, molecular biologists still need tools to help them with routine sequence analysis tasks such as restriction mapping, identifying protein coding regions or special sequence motifs, and carrying out sequence similarity searches. There are, of course, numerous shareware programs on the Web, but most of these will perform a single type of analysis (e.g., identifying restriction enzyme recognition sites) and each has a different user interface. This variability can be frustrating if one needs to carry out a variety of analyses fairly often. A convenient if more expensive alternative is to buy a comprehensive sequence analysis program designed to perform the most commonly used analyses with a single, user-friendly interface. One such software package is called MacVector, the latest release of which provides the molecular biologist with a wide variety of tools for analyzing nucleic acid and protein sequences. MacVector is designed to be used on Macintosh computers, and has a well-deserved reputation for being swift, powerful, and amazingly easy to use. A short, but by no means complete, list of nucleic acid analyses available includes restriction mapping, open reading frame searches to identify protein coding regions within a sequence, base composition and codon usage analyses, nucleic acid subsequence motif searches, primer design for PCR (polymerase chain reaction), multiple sequence alignments, and translation of open reading frames to the corresponding amino acid sequences. Protein sequences may be analyzed to determine (among other things) the molecular weight and pI (isoelectric pH) of the protein of interest and to obtain profiles of hydrophilicity, antigenicity, and secondary structure along the length of the protein. MacVector will also retrieve protein or nucleic acid sequences of interest from databases by conducting an Internet search, which is trivial to set up as well as extremely fast. Another useful feature is the ability to perform BLAST searches, where a query sequence is compared with sequences in databases accessible through the Internet, without leaving the program. Such features offer an improvement over version 6.5 [see the review of version 6.5 in ([1][1])]. New in version 7.0 is the ability to generate true phylogenetic trees with the use of distance matrix methods. Other notable features in version 7.0 include additional algorithms for identifying coding regions, and an improved multiple sequence alignment editor. BLAST searches done through MacVector are now carried out with NCBI's enhanced BLAST 2.0 programs, which permit gapped alignments. A number of small, but thoughtful, changes in the interface make the program easier to use than ever. As with earlier versions, this one is a winner. One complaint, however, concerns the Keyserver used in the network-licensed version of the program. Though the MacVector software itself is easy to use, the network installation of it is overly complicated. 1. [↵][2]1. I. Rajagopal , Science 283, 652 (1999). [OpenUrl][3][FREE Full Text][4] 2. MacVector 7.0 Genetics Computer Group Campbell, CA$2950800-876-9994 [1]: #ref-1 [2]: #xref-ref-1-1 View reference 1 in text [3]: {openurl}?query=rft.jtitle%253DScience%26rft.stitle%253DScience%26rft.issn%253D0036-8075%26rft.aulast%253DRajagopal%26rft.auinit1%253DI.%26rft.volume%253D283%26rft.issue%253D5402%26rft.spage%253D652%26rft.epage%253D653%26rft.atitle%253DSOFTWARE%253AAll-in-One%2BSequence%2BAnalysis%26rft_id%253Dinfo%253Adoi%252F10.1126%252Fscience.283.5402.652%26rft_id%253Dinfo%253Apmid%252F9988660%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [4]: /lookup/ijlink/YTozOntzOjQ6InBhdGgiO3M6MTQ6Ii9sb29rdXAvaWpsaW5rIjtzOjU6InF1ZXJ5IjthOjQ6e3M6ODoibGlua1R5cGUiO3M6NDoiRlVMTCI7czoxMToiam91cm5hbENvZGUiO3M6Mzoic2NpIjtzOjU6InJlc2lkIjtzOjEyOiIyODMvNTQwMi82NTIiO3M6NDoiYXRvbSI7czoyMjoiL3NjaS8yOTAvNTQ5MS80NzQuYXRvbSI7fXM6ODoiZnJhZ21lbnQiO3M6MDoiIjt9