Sequence Analysis of the DNA Encoding the Eco RI Endonuclease
... The source of DNA for this analysis is the plasmid, pMB1, encodestheseenzymesusingthechain-termination and derivatives constructedby recombination in zlitro. pMBl method of Sanger (Sanger,F., Nicklen, S., and Coulson, was obtained from the original clinical strain of Escherichia A. R. (1977)h c . Na ...
... The source of DNA for this analysis is the plasmid, pMB1, encodestheseenzymesusingthechain-termination and derivatives constructedby recombination in zlitro. pMBl method of Sanger (Sanger,F., Nicklen, S., and Coulson, was obtained from the original clinical strain of Escherichia A. R. (1977)h c . Na ...
Characterization of Human Immunodeficiency Virus Type 1 from a
... QIAamp Viral RNA Mini Kit (Qiagen, Valencia, CA). The V3–V5 region of env was amplified in a nested polymerase chain reaction (PCR) as described.8 A region in p24/p7 of gag was amplified in a nested PCR as described,9 except that the annealing temperature was increased to 55°C. Reverse transcription ...
... QIAamp Viral RNA Mini Kit (Qiagen, Valencia, CA). The V3–V5 region of env was amplified in a nested polymerase chain reaction (PCR) as described.8 A region in p24/p7 of gag was amplified in a nested PCR as described,9 except that the annealing temperature was increased to 55°C. Reverse transcription ...
Phylogenetic and evolutionary analyses of St. Louis encephalitis
... doi:10.1016/j.ympev.2008.02.015 ...
... doi:10.1016/j.ympev.2008.02.015 ...
Variation in biological properties of cauliflower mosaic virus clones
... passages. However, one clone (11/3-7) produced two new biotypes during its first passage suggesting that it was relatively unstable. Our results show that wild-type populations of CaMV contain a range of infectious genome variants with contrasting biological properties and differing stability. We su ...
... passages. However, one clone (11/3-7) produced two new biotypes during its first passage suggesting that it was relatively unstable. Our results show that wild-type populations of CaMV contain a range of infectious genome variants with contrasting biological properties and differing stability. We su ...
and phylogenetic characterization of Shuni virus Genomic
... temporal separation as well as possible recombination events or point mutations could affect the genotypic and phenotypic traits resulting in the observed pathogenic differences between these two strains, and thus the need to investigate the molecular biology of SHUV arose. Orthobunyaviruses are en ...
... temporal separation as well as possible recombination events or point mutations could affect the genotypic and phenotypic traits resulting in the observed pathogenic differences between these two strains, and thus the need to investigate the molecular biology of SHUV arose. Orthobunyaviruses are en ...
Local homology recognition and distance measures in linear time
... intractable for interesting values of N. We used two substitution matrices for which the underlying probabilities are readily available: BLOSUM62 and the VTML240 matrix (13). (We found integer rounded log-score matrices to have inadequate precision.) We found convergence at m = 2 (BLOSUM62) and m = ...
... intractable for interesting values of N. We used two substitution matrices for which the underlying probabilities are readily available: BLOSUM62 and the VTML240 matrix (13). (We found integer rounded log-score matrices to have inadequate precision.) We found convergence at m = 2 (BLOSUM62) and m = ...
Local homology recognition and distance
... intractable for interesting values of N. We used two substitution matrices for which the underlying probabilities are readily available: BLOSUM62 and the VTML240 matrix (13). (We found integer rounded log-score matrices to have inadequate precision.) We found convergence at m = 2 (BLOSUM62) and m = ...
... intractable for interesting values of N. We used two substitution matrices for which the underlying probabilities are readily available: BLOSUM62 and the VTML240 matrix (13). (We found integer rounded log-score matrices to have inadequate precision.) We found convergence at m = 2 (BLOSUM62) and m = ...
The polymorphism in MUC1 gene in Nelore cattle
... variations in the Nelore cattle in which the alleles with 12 and 18 repeats have not been previously described in Bos taurus Piedmontese and Italian Friesian cattle (Rasero et al. 2002). The higher frequency of the alleles with minor sizes presented in this study is in contrast to the report of Sacc ...
... variations in the Nelore cattle in which the alleles with 12 and 18 repeats have not been previously described in Bos taurus Piedmontese and Italian Friesian cattle (Rasero et al. 2002). The higher frequency of the alleles with minor sizes presented in this study is in contrast to the report of Sacc ...
S - IBIVU
... and find a homologous sequence (an ortholog or a paralog) in an annotated sequence database, i.e. a database containing sequences for which the functions are known •You then transfer the information from a putatively homologous database sequence to the query sequence This transfer of information bas ...
... and find a homologous sequence (an ortholog or a paralog) in an annotated sequence database, i.e. a database containing sequences for which the functions are known •You then transfer the information from a putatively homologous database sequence to the query sequence This transfer of information bas ...
Brief Introduction of Bioinformatics
... The technique of dynamic programming can be applied to produce global alignments via the Needleman-Wunsch algorithm, and local alignments via the Smith-Waterman algorithm. In typical usage, protein alignments use a substitution matrix to assign scores to amino-acid matches or mismatches, and a gap p ...
... The technique of dynamic programming can be applied to produce global alignments via the Needleman-Wunsch algorithm, and local alignments via the Smith-Waterman algorithm. In typical usage, protein alignments use a substitution matrix to assign scores to amino-acid matches or mismatches, and a gap p ...
Protein Sequence Alignment and Database Searching
... The Scoring Schemes or Weight Matrices For any alignment one need scoring scheme and weight matrix Important Point All algorithms to compare protein sequences rely on some scheme to score the equivalencing of each 210 possible pairs. 190 different pairs + 20 identical pairs Higher scores for ide ...
... The Scoring Schemes or Weight Matrices For any alignment one need scoring scheme and weight matrix Important Point All algorithms to compare protein sequences rely on some scheme to score the equivalencing of each 210 possible pairs. 190 different pairs + 20 identical pairs Higher scores for ide ...
Sequence analysis of 16S rRNA, gyrB and catA genes and DNA
... approximately 1200 bp PCR product besides the approximately 1500 bp specific product, making direct sequencing impossible. Sequence analyses gave interesting results. The reported 0.2 % difference between 16S rRNA gene sequences of type strains of R. qingshengii and R. jialingiae was not found, beca ...
... approximately 1200 bp PCR product besides the approximately 1500 bp specific product, making direct sequencing impossible. Sequence analyses gave interesting results. The reported 0.2 % difference between 16S rRNA gene sequences of type strains of R. qingshengii and R. jialingiae was not found, beca ...
cheng_hmm_bioinfo - University of Missouri
... SAETYRDAWGIPHLRADTPHELARAQGT--ARDRAWQLEVERHRAQGTSASFLGPEALSW ------DRLGVVTIDAANQLDAMRALGY--AQERYFEMDLMRRAPAGELSELFGAKAVDL ...
... SAETYRDAWGIPHLRADTPHELARAQGT--ARDRAWQLEVERHRAQGTSASFLGPEALSW ------DRLGVVTIDAANQLDAMRALGY--AQERYFEMDLMRRAPAGELSELFGAKAVDL ...
Slides
... and (due to the evolutionary connection) have similar function The sequence alignment problem is an optimization problem: produce the best alignment according to a ...
... and (due to the evolutionary connection) have similar function The sequence alignment problem is an optimization problem: produce the best alignment according to a ...
FASTA is a program for database searching by homology. FASTA
... S. Altchul et al developed BLAST program in 1990. The BLAST algorithm was developed as a new way to perform a sequence similarity search by an algorithm that is faster and sensitive than FASTA. This method is widely used sequence analysis facility in the world and provides similarity searching to al ...
... S. Altchul et al developed BLAST program in 1990. The BLAST algorithm was developed as a new way to perform a sequence similarity search by an algorithm that is faster and sensitive than FASTA. This method is widely used sequence analysis facility in the world and provides similarity searching to al ...
Characterization of the first cultured representative of
... centimetres thick photosynthetically active laminated microbial mat covering the bottom of the shallow hypersaline Lake 21 on the Kiritimati Atoll (Central Pacific). A unique characteristic of this cyanobacterial mat was a zone of disintegration observed at the transition between the photosynthetica ...
... centimetres thick photosynthetically active laminated microbial mat covering the bottom of the shallow hypersaline Lake 21 on the Kiritimati Atoll (Central Pacific). A unique characteristic of this cyanobacterial mat was a zone of disintegration observed at the transition between the photosynthetica ...
Database searching with DNA and protein sequences
... Many protein sequence databases are very well annotated and informationrich; the entries in these databases are cross-linked to many other databases and information sources. The most frequently used of these databases are undoubtedly Swiss-Prot8 and TrEMBL. Swiss-Prot contains a relatively small num ...
... Many protein sequence databases are very well annotated and informationrich; the entries in these databases are cross-linked to many other databases and information sources. The most frequently used of these databases are undoubtedly Swiss-Prot8 and TrEMBL. Swiss-Prot contains a relatively small num ...
Sequence analysis of 16S rRNA, gyrB and catA genes and DNA
... approximately 1200 bp PCR product besides the approximately 1500 bp specific product, making direct sequencing impossible. Sequence analyses gave interesting results. The reported 0.2 % difference between 16S rRNA gene sequences of type strains of R. qingshengii and R. jialingiae was not found, beca ...
... approximately 1200 bp PCR product besides the approximately 1500 bp specific product, making direct sequencing impossible. Sequence analyses gave interesting results. The reported 0.2 % difference between 16S rRNA gene sequences of type strains of R. qingshengii and R. jialingiae was not found, beca ...
Document
... kinase domain can make weak but relevant matches to other domain types appear very low in the hit list, so that they are missed (e.g. only appearing after 5000 kinase hits) • Sequences containing low-complexity regions, such as coiled coils and transmembrane regions, can cause an explosion of the se ...
... kinase domain can make weak but relevant matches to other domain types appear very low in the hit list, so that they are missed (e.g. only appearing after 5000 kinase hits) • Sequences containing low-complexity regions, such as coiled coils and transmembrane regions, can cause an explosion of the se ...
Presentation
... • The amino acid sequence of a protein contains information about its organelle destination. • Typically, the information can be found within a short segment of 20 to 100 amino acids preceding the cleavage site. • Signal-based methods (e.g. TargetP) can determine the cleavage site location ...
... • The amino acid sequence of a protein contains information about its organelle destination. • Typically, the information can be found within a short segment of 20 to 100 amino acids preceding the cleavage site. • Signal-based methods (e.g. TargetP) can determine the cleavage site location ...
What is similarity and homology? What is a good match? How does
... Similarity and homology Two very important basic concepts: • Similarity: Degree of likeness between two sequences, usually expressed as a percentage of similar (or identical) residues over a given length of the alignment. Can usually be easily calculated. • Homology: Statement about common evolut ...
... Similarity and homology Two very important basic concepts: • Similarity: Degree of likeness between two sequences, usually expressed as a percentage of similar (or identical) residues over a given length of the alignment. Can usually be easily calculated. • Homology: Statement about common evolut ...
Document
... the complete alignment, sequence family, or complete sequence database) • and are scaling factors to weigh the f and g contributions: if equals the number of sequences in profile, and =1 (preceding slide), then the influence of the observed frequencies in the database becomes less with an inc ...
... the complete alignment, sequence family, or complete sequence database) • and are scaling factors to weigh the f and g contributions: if equals the number of sequences in profile, and =1 (preceding slide), then the influence of the observed frequencies in the database becomes less with an inc ...
Curtovirus Infection of Chile Pepper in New Mexico
... accumulation of viral ssDNA (11). ORF C1 encodes the replication-associated protein (REP) (6), which is required for BCTV replication, and acts by binding to DNA sequences in the viral intergenic region (10). The REP protein contains regions of varying degrees of conservation among curtoviruses (9), ...
... accumulation of viral ssDNA (11). ORF C1 encodes the replication-associated protein (REP) (6), which is required for BCTV replication, and acts by binding to DNA sequences in the viral intergenic region (10). The REP protein contains regions of varying degrees of conservation among curtoviruses (9), ...
DNA Sequencing of the eta Gene Coding for
... disease, also known as the staphylococal scalded skin syndrome (SSSS). Since Melish & Glasgow (1970) established a mouse model for bioassay of SSSS, rapid progress has been made in molecular studies of the disease, and it is now well established that the exfoliative toxin (ET) is the causative agent ...
... disease, also known as the staphylococal scalded skin syndrome (SSSS). Since Melish & Glasgow (1970) established a mouse model for bioassay of SSSS, rapid progress has been made in molecular studies of the disease, and it is now well established that the exfoliative toxin (ET) is the causative agent ...