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D G Higgins

Publications and source records attributed to D G Higgins.

11 recordsLinked to original sources
PubMed1992

Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets.

Ordination is a powerful method for analysing complex data sets but has been largely ignored in sequence analysis. This paper shows how to use principal coordinates analysis to find low-dimensional representations of distance matrices derived from aligned sets of sequences. The method takes a matrix of Euclidean distances between all pairs of sequence and finds a coordinate space where the distances are exactly preserved. The main problem is to find a measure of distance between aligned sequences that is Euclidean. The simplest distance function is the square root of the percentage difference (as measured by identities) between two sequences, where one ignores any positions in the alignment where there is a gap in any sequence. If one does not ignore positions with a gap, the distances cannot be guaranteed to be Euclidean but the deleterious effects are trivial. Two examples of using the method are shown. A set of 226 aligned globins were analysed and the resulting ordination very successfully represents the known patterns of relationship between the sequences. In the other example, a set of 610 aligned 5S rRNA sequences were analysed. Sequence ordinations complement phylogenetic analyses. They should not be viewed as a complete alternative.

Amino Acid Sequence↗
PubMed1992

EMBLSCAN: fast approximate DNA database searches on compact disc.

An algorithm that allows rapid searching of nucleic acid sequences based on pregenerated index files is described. The programs and index files for searching the entire EMBL nucleotide sequence collection are being distributed on the EMBL Data Library's CD-ROM.

Algorithms↗
PubMed1992

CLUSTAL V: improved software for multiple sequence alignment.

The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added. The new software is a single program called CLUSTAL V, which is written in C and can be used on any machine with a standard C compiler. The main new features are the ability to store and reuse old alignments and the ability to calculate phylogenetic trees after alignment. The program is simple to use, completely menu driven and on-line help is provided.

Phylogeny↗
PubMed1992

GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content.

GCWIND is a microcomputer (IBM-PC compatible) program for the identification of protein-coding open reading frames. The program is similar to the FRAME program, but the latter has only been implemented for a specialized graphics package. The base compositions (%G+C) for each of the three possible reading phases through the DNA sequence are displayed separately, together with the positions of potential translation initiation and termination codons (on the leading and complementary strands), to provide an immediate representation of those regions within the sequence that have coding potential.

Codon↗
PubMed1991

The salmon gene encoding apolipoprotein A-I: cDNA sequence, tissue expression and evolution.

A cDNA encoding an apolipoprotein (Apo) has been isolated from the Atlantic salmon (Salmo salar) and sequenced. It encodes a peptide of 258 amino acids (aa), including a signal peptide of 18 aa, with 5'- and 3'-untranslated regions of the mRNA of 12 and 329 nucleotides, respectively. The protein has structural features in common with other Apo's of human and avian origin, including conserved sequences in the signal peptide and a series of internal repeats of 22 aa. The sequence has been identified as salmon Apo A-I (sApoA-I), and has 23% aa identity with human ApoA-I. Northern-blot analysis using the sApoA-I cDNA probe against total RNA prepared from several salmon tissues detects the expression of this gene in liver, intestine and muscle. A phylogenetic analysis reveals that the mammalian ApoA-I, ApoA-IV and Apo-E aa sequences are more closely related to each other than any of them are to sApoA-I. This suggests that the duplication events, from which A-I, A-IV and E arose, occurred after the divergence of the tetrapod and teleost ancestors.

Amino Acid Sequence↗
PubMed1991

Plasmodium falciparum appears to have arisen as a result of lateral transfer between avian and human hosts.

It has been proposed that the acquisition of Plasmodium falciparum by man is a relatively recent event and that the sustained presence of this disease in man is unlikely to have been possible prior to the establishment of agriculture. To establish phylogenetic relationships among the Plasmodium species and to unravel the mystery of the origin of P. falciparum, we have analyzed and compared phylogenetically the small-subunit ribosomal RNA gene sequences of the species of malaria that infect humans as well as a number of those sequences from species that infect animals. Although this comparison confirmed the three established major subgroups, broadly classed as avian, simian, and rodent, we find that the human pathogen P. falciparum is monophyletic with the avian subgroup, indicating that P. falciparum and avian parasites share a relatively recent avian progenitor. The other important human pathogen, P. vivax, is very similar to a representative of the simian group of Plasmodium. The relationship between P. falciparum and the avian parasites, and the overall phylogeny of the genus, provides evidence of an exception to Farenholz's rule, which propounds synchronous speciation between host and parasite.

Animals↗
PubMed1991

Molecular phylogeny of the subgenus Sophophora of Drosophila derived from large subunit of ribosomal RNA sequences.

RNA sequencing has been used to assess the relationships among species of the subgenus Sophophora of the genus Drosophila. Two divergent domains, D1 and D2, of the large ribosomal RNA (28S), totalling 550 nucleotides have been sequenced using the rRNA direct sequencing method. A tree has been reconstructed from the neighbor-joining algorithm and the confidence intervals were evaluated by the bootstrap procedure. Results have shown that the branching of the willistoni and saltans groups of the subgenus Sophophora is very ancient and probably predates that of the subgenus Drosophila. The other groups and subgroups of Sophophora are clustered in three main lineages: 1) the melanogaster and oriental subgroups; 2) the montium subgroup; 3) the ananassae subgroup of the melanogaster group clustered with the fima and obscura groups. Thus, in comparison with our results, several taxa of various ranks appear paraphyletic (the genus Drosophila, the subgenus Sophophora and the melanogaster group). Our biochemical phylogeny is only in partial agreement with the pattern of Throckmorton's radiations as well as with classical taxonomy, both based on morphological data.

Animals↗
PubMed1989

Replication and segregational stability of Bacillus plasmid pBAA1.

A cryptic plasmid, pBAA1, was identified in an industrial Bacillus strain. The plasmid is 6.8 kilobases in size and is present in cells at a copy number of approximately 5 per chromosome equivalent. The plasmid has been maintained under industrial fermentation conditions without apparent selective pressure and so is assumed to be partition proficient. The minimal replicon was localized to a 1.4-kilobase fragment which also contains the functions required for copy number control. The very low level of segregational instability of the minimal replicon suggests that it also contains functions involved in plasmid maintenance. Comparison with other plasmids indicates that pBAA1 belongs to the group of small gram-positive plasmids which replicate by a rolling cycle-type mechanism. A sequence was identified which is required for the efficient conversion of the single plus strand to the double-stranded form during plasmid replication. Deletion of this sequence resulted in a low level of segregational plasmid instability.

Amino Acid Sequence↗