A comprehensive sequence analysis program for the IBM personal computer

Queen, Cary; Korn, Laurence Jay

doi:10.1093/nar/12.1part2.581

Cited by 607 publications

(219 citation statements)

References 39 publications

(25 reference statements)

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“…The DNA sequence analysis was performed using the Beckman Microgenie Software (Queen & Korn, 1984) and the Sequence Analysis Package (Stephens, 1985) on an IBM PC AT computer.…”

Section: Methodsmentioning

confidence: 99%

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Porcine Parvovirus: DNA Sequence and Genome Organization

Ranz

Manclús

Diaz-Aroca

et al. 1989

Journal of General Virology

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SUMMARYWe have determined the nucleotide sequence of an almost full-length clone of porcine parvovirus (PPV). The sequence is 4973 nucleotides (nt) long. The 3' end of virion DNA shows a Y-shaped configuration homologous to rodent parvoviruses. The 5' end of virion DNA shows a repetition of 127 nt at the carboxy terminus of the capsid proteins. The overall organization of the PPV genome is similar to those of other autonomous parvoviruses. There are two large open reading frames (ORFs) that almost entirely cover the genome, both located in the same frame of the complementary strand. The left ORF encodes the non-structural protein NS1 and the right ORF encodes the capsid proteins (VP1, VP2 and VP3). Promoter analysis, location of splicing sites and putative amino acid sequences for the viral proteins show a high homology of PPV with feline panleukopenia virus and canine parvoviruses (FPV and CPV) and rodent parvovirus. Therefore we conclude that PPV is related to the Kilham rat virus (KRV) group of autonomous parvoviruses formed by KRV, minute virus of mice, Lu III, H-I, FPV and CPV.

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“…The DNA sequence analysis was performed using the Beckman Microgenie Software (Queen & Korn, 1984) and the Sequence Analysis Package (Stephens, 1985) on an IBM PC AT computer.…”

Section: Methodsmentioning

confidence: 99%

“…The final DNA sequence of the PPV genome was analysed by the computer programs already mentioned (Queen & Korn, 1984;Stephens, 1985). The potential coding domains for both the complementary strand (C strand, plus polarity) and the viral strand (V strand, minus polarity) are shown in Fig.…”

Section: Genome Organization and Assignment Of Pp V Genesmentioning

confidence: 99%

Porcine Parvovirus: DNA Sequence and Genome Organization

Ranz

Manclús

Diaz-Aroca

et al. 1989

Journal of General Virology

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“…cDNA inserts were subcloned into M13mp19 [lo] and single strands were sequenced on field gradient gels [ll] by the dideoxynucleoside triphosphate chaintermination method [12]. Sequence data were compiled and analyzed with computer assistance [13].…”

Section: A Sp-4mentioning

confidence: 99%

Human monocyte chemoattractant protein‐1 (MCP‐1) Full‐length cDNA cloning, expression in mitogen‐stimulated blood mononuclear leukocytes, and sequence similarity to mouse competence gene JE

et al. 1989

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The purpose of this work was to analyze cDNA encoding human monocyte chemoattractant protein-l (MCP-I), previously isolated from glioma cell line culture fluid. Screening of a cDNA library from total poly(A) RNA of glioma cell line U-105MG yielded a clone that coded for the entire MCP-1. Nucleotide sequence analysis and comparison with the amino acid sequence of purified MCP-1 showed that the cDNA clone comprises a 53-nucleotide 5'-non-coding region, an open reading frame coding for a 99-residue protein of which the last 76 residues correspond exactly to pure MCP-1, and a 389nucleotide 3'-untranslated region. The hydrophobicity of the first 23 residues is typical of a signal peptide. Southern blot analysis of human and animal genomic DNA showed that there is a single MCP-1 gene, which is conserved in several primates. MCP-1 mRNA was induced in human peripheral blood mononuclear leukocytes (PBMNLs) by PHA, LPS and IL-l, but not by IL-2, TNF, or IFN-y. Among proteins with similar sequences, the coding regions of MCP-1 and mouse JE show 68% identity. This suggests that MCP-1 is the human homologue of the mouse competence gene JE.

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“…Computer programs developed by Queen and Korn (26) and Staden (27) were used to assemble and analyse the sequence. Molecular weights calculated by these programs differed slightly.…”

Section: Dna §Eqnm_ Analysismentioning

confidence: 99%

“…Molecular weights calculated by these programs differed slightly. Those reported in this paper were calculated according to (26).…”

Section: Dna §Eqnm_ Analysismentioning

confidence: 99%