Types Of Sequence Data Research Articles

Covariability of V3 loop amino acids.

We reanalyzed for covariability a set of 308 human immunodeficiency virus type 1 (HIV-1) V3 loop amino acid sequences from the B envelope sequence subtype previously analyzed by Korber et al.,1 as well as a new set of 440 sequences that also included substantial numbers of sequences from subtypes A, D, and E. We used the measure employed by Korber et al., essentially the likelihood ratio statistic for independence, plus two additional measures as well as clade information to examine the new set and both data sets simultaneously. We set forth the following conclusions and observations. The eight most highly connected sites identified through these statistical approaches included all of the six residues previously shown to have determining roles in structure, immunologic recognition, virus phenotype, and host range; each of the seven pairs of covariant sites found by Korber were signaled by our additional two measures in the set of 308 sequences, although 2 or 3 dropped out of the examination of the set of 440 when the requirement of stringent significance was applied for some or all of the three tests, respectively; using the same criteria, a total of 20 (including 5 Korber et al. pairs) or a total of 6 (including 4 Korber et al. pairs) were found when the set of 440 was added. Several limitations to statistical analysis of this type of HIV sequence data were also noted. For example, the data sets were, by historical necessity, collected haphazardly. For example, it was not possible to separate substantially sized groups out according to time of or since infection, disease status, antiviral treatment, geography, etc. There was also an enormous "wealth of significance" within the data. For example, for one measure the 440 data set showed 233 of the 465 pairs of sites with a likelihood ratio statistic of < 0.001. Last, most sites had consensus amino acids in 80% or more of the sequences; hence, there was an absence of data on many combinations of amino acids. Given the observed linkage between sites shown to be covariable and those known to have critical biological function, the statistical approaches we and Korber et al. have outlined may find use in predicting critical structural features of HIV proteins as targets for therapeutic intervention.

Submission of nucleotide sequence data to EMBL/GenBank/DDBJ.

This review outlines the various methods available for submitting sequence data to the EMBL Nucleotide Sequence Database. Depending on the type of sequence data and the facilities available to the submitter, one method may be more suitable than another. Recent developments have been the World Wide Web submission tool, procedures for bulk submissions and genome projects.

DNA strider

DNA Strider is a user-friendly Macintosh program designed for analysis of molecular sequence data. The program shows great versatility in choice of genetic codes, restriction enzymes, algorithms for hydropathy plots, and interconversions between types of sequence data. It is very straightforward and interacts well with other sequence and phylogenetic analysis packages, importing and exporting data easily. The graphic outputs can be used directly for manuscript-quality figures, or exported to more sophisticated text or graphic programs.

Description and improvement of iterative program transformations

Our framework is a programming method whose main idea consists in solving a problem statically and explicitly before taking some execution details into account. Within the framework of the methodology for constructing a program, we are often compelled to introduce intermediate values. We prove that in the case of sequential languages, and especially when they are sequence data types, those intermediates do not need to be effectively constructed. This aspect of the problem is obviously connected with efficiency. We suggest program transformation as a possible means of eliminating useless intermediates in the case of sequential languages. This paper follows [12] and aims at describing a program construction method, a set of transformations rules and their application with an example.