CS 6293 Advanced Topics: Translational Bioinformatics
... only inside the living cells of other organisms [6]. Viruses can infect all types of life forms, from animals and plants to bacteria and archaea. • Basic structural characteristics, such as genome type, virion shape and replication site, generally share the same features among virus species within ...
... only inside the living cells of other organisms [6]. Viruses can infect all types of life forms, from animals and plants to bacteria and archaea. • Basic structural characteristics, such as genome type, virion shape and replication site, generally share the same features among virus species within ...
THE IDENTIFICATION AND CHARACTERISATION OF THE
... showed a high similarity to an amino acid adenylation protein in Granuliella mallensis MP5ACIX8 (YP_00507340.1) with an amino acid similarity of 57%, an amino acid adenylation protein in Streptomyces griseus XYLEBKG1 (YP_08236938.1) with an amino acid similarity of 60% and a NRPS in Streptomyces net ...
... showed a high similarity to an amino acid adenylation protein in Granuliella mallensis MP5ACIX8 (YP_00507340.1) with an amino acid similarity of 57%, an amino acid adenylation protein in Streptomyces griseus XYLEBKG1 (YP_08236938.1) with an amino acid similarity of 60% and a NRPS in Streptomyces net ...
Milestone10
... You should submit these 21 sequences to the Gibbs Motif Sampler web server. These 21 sequences come from the same genome, why do we expect common patterns in these sequences? Since the microarray data suggests that the genes are co-expressed, i.e., they are expressed under the same conditions, the g ...
... You should submit these 21 sequences to the Gibbs Motif Sampler web server. These 21 sequences come from the same genome, why do we expect common patterns in these sequences? Since the microarray data suggests that the genes are co-expressed, i.e., they are expressed under the same conditions, the g ...
R4, a non-LTR retrotransposon specific to the
... extend only a few base pairs along the DNA, thus they insert at numerous locations throughout the host genome. When these elements fall within or near transcription units they can cause significant detrimental effects on the host. Less well appreciated is the risk that this random method of insertio ...
... extend only a few base pairs along the DNA, thus they insert at numerous locations throughout the host genome. When these elements fall within or near transcription units they can cause significant detrimental effects on the host. Less well appreciated is the risk that this random method of insertio ...
Nomenclature for incompletely specified bases in nucleic acid
... the need for presenting a schematic summary of the sequence features. For instance, sequences recognized by the RNA polymerase of Escherichia coli may be presented as the juxtaposition of two sequences 5'-AA(A or T)NTNNN(C or G)TTGACA-3' and 5'-(T or G)NNTATAAT-3' separated by 13-16 nucleotides (ada ...
... the need for presenting a schematic summary of the sequence features. For instance, sequences recognized by the RNA polymerase of Escherichia coli may be presented as the juxtaposition of two sequences 5'-AA(A or T)NTNNN(C or G)TTGACA-3' and 5'-(T or G)NNTATAAT-3' separated by 13-16 nucleotides (ada ...
Computational neuroanatomy and co
... quantitative techniques and software for data analysis. The present paper reviews recent developments that have been applied to co-expression studies in the mouse brain and are publicly available for use on the Web [8] and on the desktop [9]. On the other hand, lists of condition-related genes are n ...
... quantitative techniques and software for data analysis. The present paper reviews recent developments that have been applied to co-expression studies in the mouse brain and are publicly available for use on the Web [8] and on the desktop [9]. On the other hand, lists of condition-related genes are n ...
Ch. 13 Bioengineering
... • Separating DNA – In gel electrophoresis, DNA fragments are placed at one end of a porous gel, and an electric voltage is applied to the gel. – When the power is turned on, the negatively-charged DNA molecules move toward the positive end of the gel. ...
... • Separating DNA – In gel electrophoresis, DNA fragments are placed at one end of a porous gel, and an electric voltage is applied to the gel. – When the power is turned on, the negatively-charged DNA molecules move toward the positive end of the gel. ...
Production of industrially relevant compounds in prokaryotic
... T3 population With the P3 and P4 gates indicated. FIG. 9B shoWs the initial ?uorescence of the sorted P4 population. FIG. 9C shoWs the initial ?uorescence of the sorted P3 popu lation. ...
... T3 population With the P3 and P4 gates indicated. FIG. 9B shoWs the initial ?uorescence of the sorted P4 population. FIG. 9C shoWs the initial ?uorescence of the sorted P3 popu lation. ...
Biology and computers
... coil regions (not essential for structure) and therefore gap penalties are reduced reduced for such stretches. Gap penalties for closely related sequences are lowered compared to more distantly related sequences (“once a gap always a gap” rule). It is thought that those gaps occur in regions that do ...
... coil regions (not essential for structure) and therefore gap penalties are reduced reduced for such stretches. Gap penalties for closely related sequences are lowered compared to more distantly related sequences (“once a gap always a gap” rule). It is thought that those gaps occur in regions that do ...
BAC White Paper - Faculty Web Sites at the University of Virginia
... gastrula and neurula stages, an issue which becomes important for example, in making genetic chimeras. Third, at least at present, transgenic technology is more advanced in the frog system; one can readily generate, at low cost, hundreds of transgenic animals per day. Finally, the zebrafish genome i ...
... gastrula and neurula stages, an issue which becomes important for example, in making genetic chimeras. Third, at least at present, transgenic technology is more advanced in the frog system; one can readily generate, at low cost, hundreds of transgenic animals per day. Finally, the zebrafish genome i ...
Epstein-Barr virus exploits intrinsic B-lymphocyte
... In contrast to LCL enhancer sites where RELA-ETS, EBFRUNX, and EBF were associated with higher H3K4me1 signals (P < 0.01) versus ETS, RBPJ, and repressive RUNX (Fig. 1C, Left), and as a single-factor EBF had the largest up-regulatory effect (Table S4), at promoter sites, EBNA2 and RELA-ETS, ETS, and ...
... In contrast to LCL enhancer sites where RELA-ETS, EBFRUNX, and EBF were associated with higher H3K4me1 signals (P < 0.01) versus ETS, RBPJ, and repressive RUNX (Fig. 1C, Left), and as a single-factor EBF had the largest up-regulatory effect (Table S4), at promoter sites, EBNA2 and RELA-ETS, ETS, and ...
Multiple Sequence Alignment
... coil regions (not essential for structure) and therefore gap penalties are reduced reduced for such stretches. ! Gap penalties for closely related sequences are lowered compared to more distantly related sequences (“once a gap always a gap” rule). It is thought that those gaps occur in regions tha ...
... coil regions (not essential for structure) and therefore gap penalties are reduced reduced for such stretches. ! Gap penalties for closely related sequences are lowered compared to more distantly related sequences (“once a gap always a gap” rule). It is thought that those gaps occur in regions tha ...
Investigation Of Haemoglobinopathy.
... ► Scanning allows quantification of the hemoglobin present, bands are seen by ...
... ► Scanning allows quantification of the hemoglobin present, bands are seen by ...
PDF ( 33 ) - DergiPark
... Prize in Chemistry of 2012, indicated that GPRCs are the detectors from which the sensory receptor cells directly receive external signals (1). GPRC5D is a member of the retinoic acid inducible gene-1 (RAIG1) family, which comprises 4 genes (RAIG1, GPRC5B, GPRC5C, and GPRC5D) (2).The RAIG-1 gene fam ...
... Prize in Chemistry of 2012, indicated that GPRCs are the detectors from which the sensory receptor cells directly receive external signals (1). GPRC5D is a member of the retinoic acid inducible gene-1 (RAIG1) family, which comprises 4 genes (RAIG1, GPRC5B, GPRC5C, and GPRC5D) (2).The RAIG-1 gene fam ...
Investigation Of Haemoglobinopathy.
... ► Scanning allows quantification of the hemoglobin present, bands are seen by ...
... ► Scanning allows quantification of the hemoglobin present, bands are seen by ...
Characterization of the Plasmid-Encoded Arsenic Salts Resistance
... Both the N-terminal and C-terminal contained the glycinerich clusters, G15KGGVGKTS23 and G335KRCVGKT343, suggesting that the ArsA protein is the catalytic subunit of an arsenate-translocating ATPase [4]. The predicted ArsA protein also contained two independent domains with 32% homology, possibly du ...
... Both the N-terminal and C-terminal contained the glycinerich clusters, G15KGGVGKTS23 and G335KRCVGKT343, suggesting that the ArsA protein is the catalytic subunit of an arsenate-translocating ATPase [4]. The predicted ArsA protein also contained two independent domains with 32% homology, possibly du ...
Histone Modifications and Cancer
... Histone acetylation/deacetylation • Acetylation/deacetylation of defined lysine residues of H3, H4, H2A and H2B histones; • Catalyzed by histone acetyltransferase/deacetylase ...
... Histone acetylation/deacetylation • Acetylation/deacetylation of defined lysine residues of H3, H4, H2A and H2B histones; • Catalyzed by histone acetyltransferase/deacetylase ...
ONE
... through the GenBank, databases for DNA sequences. Neuhaus and Link (1987) found that a segment near the carboxyl terminus of the derived Sinapsis alba matK polypeptide was structurally related to portions of the maturase-like polypeptides of introns of the mitochordrial cytochrome c oxidase subunit ...
... through the GenBank, databases for DNA sequences. Neuhaus and Link (1987) found that a segment near the carboxyl terminus of the derived Sinapsis alba matK polypeptide was structurally related to portions of the maturase-like polypeptides of introns of the mitochordrial cytochrome c oxidase subunit ...
![[15] Recombineering: In Vivo Genetic Engineering in E. coli, S](http://s1.studyres.com/store/data/004714893_1-0f26f8c0250e6700b822c560c415d9ab-300x300.png)
[15] Recombineering: In Vivo Genetic Engineering in E. coli, S
... a large disposable pipette tip or gentle shaking. A vortex must not be used for this or subsequent steps as cells in H2O are fragile. After the cells are suspended, an additional 30 ml of ice‐cold sterile distilled water is added to each tube and gently rocked to mix before pelleting again at 4600 ...
... a large disposable pipette tip or gentle shaking. A vortex must not be used for this or subsequent steps as cells in H2O are fragile. After the cells are suspended, an additional 30 ml of ice‐cold sterile distilled water is added to each tube and gently rocked to mix before pelleting again at 4600 ...
No Slide Title
... 1. Compute optimal pairwise alignments to get an upper bound on any pair of alignments. MSA can’t do any better than sum of optimal pairwise alignments. 2. Create heuristic multiple alignment in ad hoc fashion to create a lower bound on MA score (using a guide tree). 3. Search N-dimensional scoring ...
... 1. Compute optimal pairwise alignments to get an upper bound on any pair of alignments. MSA can’t do any better than sum of optimal pairwise alignments. 2. Create heuristic multiple alignment in ad hoc fashion to create a lower bound on MA score (using a guide tree). 3. Search N-dimensional scoring ...
Agrobacterium tumefaciens T DNA mediated transformation of
... marker (AmpR), to facilitate plasmid rescue in E. coli of T-DNA junction sequences containing E. festucae DNA. Plasmid pYT6 contains a hygromycin resistance cassette between the left and right T-DNA borders, a KanR bacterial selectable marker, pBR322 (ColE1) origin of replication (ori), the cis acti ...
... marker (AmpR), to facilitate plasmid rescue in E. coli of T-DNA junction sequences containing E. festucae DNA. Plasmid pYT6 contains a hygromycin resistance cassette between the left and right T-DNA borders, a KanR bacterial selectable marker, pBR322 (ColE1) origin of replication (ori), the cis acti ...
Evolution by leaps: gene duplication in bacteria | SpringerLink
... families in large data sets like collections of whole genome sequences, we planned to examine a few paralogous groups in a limited number of bacteria where the great majority of the functions of the individual proteins in each family is known. We wanted to see what kind of impact expansion of a fami ...
... families in large data sets like collections of whole genome sequences, we planned to examine a few paralogous groups in a limited number of bacteria where the great majority of the functions of the individual proteins in each family is known. We wanted to see what kind of impact expansion of a fami ...
Characterization of the Cobalamin (Vitamin B12) Biosynthetic Genes
... cobalamin synthesis (Table 2). (An additional ORF extends from the first nucleotide of the sequence to nucleotide 690; this ORF encodes the C-terminal portion of the pocR regulatory gene [17, 85] and will be discussed below.) Genes assigned to part I of the pathway are assigned cbi designations (syn ...
... cobalamin synthesis (Table 2). (An additional ORF extends from the first nucleotide of the sequence to nucleotide 690; this ORF encodes the C-terminal portion of the pocR regulatory gene [17, 85] and will be discussed below.) Genes assigned to part I of the pathway are assigned cbi designations (syn ...
A tale of two functions: enzymatic activity and
... electropositive surface potential, whereas the rest of the protein has a net electronegative surface potential (6). Zinc-finger domains are commonly associated with nucleic acid-binding proteins and previous studies have shown that CT does bind DNA, albeit non-specifically (7). Notably, DNA binding in ...
... electropositive surface potential, whereas the rest of the protein has a net electronegative surface potential (6). Zinc-finger domains are commonly associated with nucleic acid-binding proteins and previous studies have shown that CT does bind DNA, albeit non-specifically (7). Notably, DNA binding in ...
DNA Sequencing of the eta Gene Coding for
... Fig. 4. Inverted sequences in the 5' and 3' flanking regions of the ETA coding sequence. (a, b) Inverted sequences upstream of the presumed SD sequence. Promoter-like sequences (- 35 and - 10 regions) are indicated by lines above the respective hexanucleotides. Note that both -10 regions overlap the ...
... Fig. 4. Inverted sequences in the 5' and 3' flanking regions of the ETA coding sequence. (a, b) Inverted sequences upstream of the presumed SD sequence. Promoter-like sequences (- 35 and - 10 regions) are indicated by lines above the respective hexanucleotides. Note that both -10 regions overlap the ...
Promoter (genetics)
In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5' region of the sense strand).Promoters can be about 100–1000 base pairs long.