Genome sequence of a reassortant strain of bluetongue virus serotype 23 from western India

The full genome sequence (19,177 bp) of an Indian strain (IND1988/02) of bluetongue virus (BTV) serotype 23 was determined. This virus was isolated from a sheep that had been killed during a severe bluetongue outbreak that occurred in Rahuri, Maharashtra State, western India, in 1988. Phylogenetic analyses of these data demonstrate that most of the genome segments from IND1988/02 belong to the major "eastern" BTV topotype. However, genome segment 5 belongs to the major "western" BTV topotype, demonstrating that IND1988/02 is a reassortant. This may help to explain the increased virulence that was seen during this outbreak in 1988. Genome segment 5 of IND1988/02 shows >99% sequence identity with some other BTV isolates from India (e.g., BTV-3 IND2003/08), providing further evidence of the existence and circulation of reassortant strains on the subcontinent.     

SDSE: A software package to simulate the evolution of a pair of DNA sequences

An algorithm to simulate DNA sequence evolution under a generalstochastic model, including as particular cases all the previouslyused schemes of nucleotide substitution, is described. The simulationis carried out on finite, variable length, DNA sequences througha strict stochastic process, according to the particular substitutionrates imposed by each scheme. Five FORTRAN programs, runningon an IBM PC and compatibles, carry out all the tasks neededfor the simulation. They are menu driven and interfaced to thesystem through a principal menu. All sequence data files usedand generated by the SDSE package conform to the standard GenBankdatabase format, thus allowing the use of any sequence retrievedfrom this databank, as well as the application of other packagesto analyse, manipulate or retrieve simulated sequences. Received on August 23, 1988; accepted on November 15, 1988     

A program for template matching of protein sequences

The matching of a template to a protein sequence is simplifiedby treating it as a special case of sequence alignment. Restrictionof the distances between motifs in the template controls againstspurious matches within very long sequences. The program usingthis algorithm is fast enough to be used in scanning large databasesfor sequences matching a complex template. Received on August 17, 1987; accepted on January 11, 1988     

Nucleotide Sequence of cDNA for Concanavalin A from Canavalia gladiata Seeds

We have determined the nucleotide sequence of Con A cDNA forconcanavalin A (Con A) from Canavalia gladiata using a plasmid(pCONAl) that was isolated previously [Eur. J. Bio-chem. (1988)170: 515-520]. This sequence contains a 870-bp open readingframe, a 63-bp 5'-un-translated region and a 99-bp 3'-untranslatedregion. DNA blot analysis suggested that Con A is encoded bya small gene family. In contrast to the case of canavalin, thenucleotide sequence and the genomic organization of Con A geneare highly conserved between C. gladiata and C. ensifor-mis. (Received August 4, 1988; Accepted November 21, 1988)     

Multiple DNA and protein sequence alignment on a workstation and a supercomputer

This paper describes a multiple alignment method using a workstationand supercomputer. The method is based on the alignment of aset of aligned sequences with the new sequence, and uses a recursiveprocedure of such alignment. The alignment is executed in areasonable computation time on diverse levels from a workstationto a supercomputer, from the viewpoint of alignment resultsand computational speed by parallel processing. The applicationof the algorithm is illustrated by several examples of multiplealignment of 12 amino acid and DNA sequences of HIV (human immunodeficiencyvirus) env genes. Colour graphic programs on a workstation andparallel processing on a supercomputer are discussed. Received on April 26, 1988; accepted on July 7, 1988     

Plasmodium falciparum: an intervening sequence in the GBP 130/96 tR gene

The 96 tR antigen is a heat stable protein produced during the late stages of the intraerythrocytic development of the malaria parasite Plasmodium falciparum and is released into the culture supernatant or the sera of infected patients at the time of schizont rupture. This antigen, identified as a putative protective antigen, was shown to be identical to the glycophorin-binding protein GBP 130 (Perkins 1988, Bonnefoy et al. 1988). We report here that the gene contains a small undescribed intervening sequence located immediately after the sequence coding for the signal sequence. This shows that in P. falciparum, all the genes described so far coding for proteins exported outside the parasitophorous vacuole share a common organization.     

A set of Macintosh computer programs for the design and analysis of synthetic genes

Computer programs that can be used for the design of syntheticgenes and that are run on an Apple Macintosh computer are described.These programs determine nucleic acid sequences encoding aminoacid sequences. They select DNA sequences based on codon usageas specified by the user, and determine the placement of basechanges that can be used to create restriction enzyme siteswithout altering the amino acid sequence. A new algorithm forfinding restriction sites by translating the restriction endonucleasetarget sequence in all three reading frames and then searchingthe given peptide or protein amino acid sequence with theseshort restriction enzyme peptide sequences is described. Examplesare given for the creation of synthetic DNA sequences for thebovine prethrombin-2 and ribonuclease A genes Received on October 18, 1988; accepted on December 9, 1988     

New analytical tool for analysis of splice site sequence determinants

A new analytical method has been used to examine the set of40 exon/intron boundaries within the rat embryonic myosin heavychain (MHC_emb) gene. It has also been applied to an additionalset of 850 splice sequences selected from GenBank. Strong evidenceis obtained for the involvement of 3' ends but not 5' ends ofexon sequences in splice site recognition. It can be determinedthat signal sequences of 5' intron ends concentrate near thesplice borders, while the distributions of the 3' intron endshave a diffuse character. The possibility of re-interpretingsome known features, in terms of the absence of certain elementsrather than the presence of elements forming sequence determinants,is discussed. The analysis undertaken enabled us to work outa more detailed set of recognition sequence requirements forthe splicing of nuclear pre-mRNA. In addition to requirementswhich have already been established we suggest the following:the ‘AG-absence’ in the immediate 3' terminal intronsequences; and a minimal match between a particular sequenceand the known exon/intron consensus sequence of 5' splice junctions. Received on March 22, 1988; accepted on November 19, 1988     

A finite state machine algorithm for finding restriction sites and other pattern matching applications

Existing algorithms for finding restriction endonuclease recognitionsites use brute-force algorithms which run in time 0(NM) whereN is the number of nucleotides in the sequence under analysisand M is the total number of nucleotides in all the differentsites being searched for. This paper presents a deterministicfinite state machine algorithm which runs in time 0(N). Memoryuse can be as high as 0(M⁴) but a slight modification to thebasic algorithm can impose a theoretical upper bound of 0(M)at the cost of some added complexity in the execution of thestate machine. The algorithm can operate with a single passthrough the sequence under analysis, with no need to back upor (for non-circular sequences) store more than a single inputcharacter at a time. This type of algorithm can be adapted tomany pattern-matching tasks and is simple enough to implementin hardware that it could, for example, be built into a diskcontroller as part of a specialized database machine. Received on April 14, 1988; accepted on June 16, 1988     

GELENT: a sequence gel entry program for keyboard and sonic digitizer input

A program is described for sequence data entry which allowsflexible program control by responding to both the keyboardand a sonic digitizer concurrently. Simplification of the initializationstage of each gel reading has been achieved, in comparison withother programs. Received on July 7, 1988; accepted on January 10, 1989     

The primary sequence of the PFK-1 inactivating zinc-binding protein as deduced from cDNA sequencing. Identity of the zinc-binding protein with rat parathymosin

We have recently described the sequence of the Zn2+-binding domain (43 amino acid residues) of a newly detected Zn2+-binding protein which reversibly inactivates phosphofructokinase-1 in a Zn2+-dependent manner [(1986) J. Biol. Chem. 269, 5895-5900; (1988) Eur. J. Biochem. 177, 561-568]. Here, we describe the primary sequence of this protein based on a full-length cDNA. A sequence comparison reveals the identity of the Zn2+-binding protein with a protein called parathymosin-alpha.     

The frequency of oligonucleotides in mammalian genic regions

The large body of nucleic acid sequence data now available offersa unique opportunity for the characterization of individualoligonucleotides which may be specific to sequence functionaldomains. We have prepared algorithms for the study of the frequencydistribution of all oligonucleotides of length 2–6 inDNA sequences. We have implemented them in the study of 634mammalian DNA sequences spanning 1.782 Mb, and have obtainedthe distribution of the ratio between the observed frequencyof oligonucleotides and their expected frequency based on independentnucleotide probabilities. We then studied the distribution ofoligonucleotides (or k-tuples) of each length in a subset of129 complete mammalian genes spanning 0.607 Mb. Eight distinctgenomic regions, namely 5'-non-transcribed, first exon, firstintron, intermediate exons, intermediate introns, last intron,last exon and 3non-transcribed, were considered. We observedthat some oligonucleotides show a statistical behaviour anda regional distribution similar to that of known signal sequences.Moreover the frequency distribution of oligonucleotides of length5 and 6 tends to become bimodal, indicating the existence ofa population of very frequent oligonucleotides. Received on June 21, 1988; accepted on October 14, 1988     

Profile scanning for three-dimensional structural patterns in protein sequences

Profile analysis measures the similarity between a target sequenceand a group of aligned sequences (the probe). The probe sequencesare used to produce a position-specific scoring table (the profile)that can be aligned with any sequence (the target) using standarddynamic programming methods. We are developing a library ofprofiles, each describing a different structural motif. Thisallows any target sequence to be rapidly scanned for the presenceof structural motifs. Levels of significance for the comparisonof target sequences with the profile are determined in advance,permitting an objective decision to be made as to whether aprotein is likely to possess a structural motif. Received on July 17, 1987; accepted on January 4, 1988     

Drosophila laminin: sequence of B2 subunit and expression of all three subunits during embryogenesis

In a previous study, we described the cloning of the genes encoding the three subunits of Drosophila laminin, a substrate adhesion molecule, and the cDNA sequence of the B1 subunit (Montell and Goodman, 1988). This analysis revealed the similarity of Drosophila laminin with the mouse and human complexes in subunit composition, domain structure, and amino acid sequence. In this paper, we report the deduced amino acid sequence of the B2 subunit. We then describe the expression and tissue distribution of the three subunits of laminin during Drosophila embryogenesis using both in situ hybridization and immunolocalization techniques, with particular emphasis on its expression in and around the developing nervous system.     

The SWISS-PROT protein sequence data bank: current status.

SWISS-PROT is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1988, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library. The SWISS-PROT protein sequence data bank consist of sequence entries. Sequence entries are composed of different lines types, each with their own format. For standardization purposes the format of SWISS-PROT follows as closely as possible that of the EMBL Nucleotide Sequence Database. A sample SWISS-PROT entry is shown in Figure 1.     

The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database.

From its origin, the PIR has aspired to support research in computational biology and genomics through the compilation of a comprehensive, quality controlled and well-organized protein sequence information resource. The resource originated with the pioneering work of the late Margaret O. Dayhoff in the early 1960s. Since 1988, the Protein Sequence Database has been maintained collaboratively by PIR-International, an association of macromolecular sequence data collection centers dedicated to fostering international cooperation as an essential element in the development of scientific databases. The work of the resource is widely distributed and is available on the World Wide Web, via FTP, E-mail server, CD-ROM and magnetic media. It is widely redistributed and incorporated into many other protein sequence data compilations including SWISS-PROT and theEntrezsystem of the NCBI.