CAPSTONE - Bioinformatics at School of Informatics
... Motivation • Comparative Genomics involves determination of the synteny regions between two or more genomes. • Synteny is the preserved order of genes between related species. • Currently available tools like SynBrowse*, provide visualization of synteny between genomes but it involves pre-computatio ...
... Motivation • Comparative Genomics involves determination of the synteny regions between two or more genomes. • Synteny is the preserved order of genes between related species. • Currently available tools like SynBrowse*, provide visualization of synteny between genomes but it involves pre-computatio ...
Why does the giraffe have such a long neck? Analysis zeroes in on
... Most of the genes Cavener and Agaba found help determine how the bodies of other animals form. This supports the idea that tweaking these genes could change an animal's physical qualities. For example, a small change in genes could make a donkey-like creature incredibly tall. The scientists found so ...
... Most of the genes Cavener and Agaba found help determine how the bodies of other animals form. This supports the idea that tweaking these genes could change an animal's physical qualities. For example, a small change in genes could make a donkey-like creature incredibly tall. The scientists found so ...
Lesson B: What Can Pseudogenes Tell Us About Common Ancestry
... Suppose a mutation that inactivates a gene becomes common over generations so that eventually all the individuals (descendants of the original mutation carrier) carry only the inactive version of the gene. Since other mutations are possible over time, two distant descendants would not necessarily re ...
... Suppose a mutation that inactivates a gene becomes common over generations so that eventually all the individuals (descendants of the original mutation carrier) carry only the inactive version of the gene. Since other mutations are possible over time, two distant descendants would not necessarily re ...
1995 Broad et al: CURRENT STATE OF THE NEW ZEALAND
... The increased fecundity of sheep with the Booroola gene is attributable to a mutation at a single locus which segregates in the classical Mendelian fashion. However, it is known that many of the production and performance traits segregate in a more complex, quantitative manner. The “whole genome scr ...
... The increased fecundity of sheep with the Booroola gene is attributable to a mutation at a single locus which segregates in the classical Mendelian fashion. However, it is known that many of the production and performance traits segregate in a more complex, quantitative manner. The “whole genome scr ...
Document
... 10. Sequence the Factor VIII cDNA Clone and Compare With Factor VIII Gene Sequence to Map its Anatomy (I.e., introns, exons, swtiches) and Ensure That it Contains the Complete Protein Coding Sequence 11. Use Factor VIII cDNA and/or Genome Fragments as a Probe to Find RFLP Markers For Disease Alleles ...
... 10. Sequence the Factor VIII cDNA Clone and Compare With Factor VIII Gene Sequence to Map its Anatomy (I.e., introns, exons, swtiches) and Ensure That it Contains the Complete Protein Coding Sequence 11. Use Factor VIII cDNA and/or Genome Fragments as a Probe to Find RFLP Markers For Disease Alleles ...
In search of essentiality: Mollicute-specific genes
... would have fallen into the T category (signal transduction mechanisms),and four genes could not be classified (Table 1). Most of the 210 genes shared by Mollicutes have a known function or at least a predicted function. Among all BBHs only 7 clusters are formed by conserved hypothetical or only hypo ...
... would have fallen into the T category (signal transduction mechanisms),and four genes could not be classified (Table 1). Most of the 210 genes shared by Mollicutes have a known function or at least a predicted function. Among all BBHs only 7 clusters are formed by conserved hypothetical or only hypo ...
SUPPORTING INFORMATION Manipulating fatty acid biosynthesis
... Protein sequences of Cr-cACP (ACP2, Q6UKY5_CHLRE), Cr-mACP (ACP1, Q6UKY4_CHLRE), CrTE (FAT1, A8HY17_CHLRE), ChTE (FATB2, Q39514_CUPHO) and UcTE (FATB1, Q41635) were obtained from the UniProt database. Sequence alignments were conducted using TCOFFEE [1] and ESPRIPT [2], based on the secondary struct ...
... Protein sequences of Cr-cACP (ACP2, Q6UKY5_CHLRE), Cr-mACP (ACP1, Q6UKY4_CHLRE), CrTE (FAT1, A8HY17_CHLRE), ChTE (FATB2, Q39514_CUPHO) and UcTE (FATB1, Q41635) were obtained from the UniProt database. Sequence alignments were conducted using TCOFFEE [1] and ESPRIPT [2], based on the secondary struct ...
Genetic recombination and mutations - formatted
... The answer to the question as to “How does the genetic variation arise?” lies in understanding the phenomena of mutation. Mutation can be defined as the occurrence of any change in the sequence of nucleic acid or any change in the chromosomal structure. Mutations can also be defined as heritable cha ...
... The answer to the question as to “How does the genetic variation arise?” lies in understanding the phenomena of mutation. Mutation can be defined as the occurrence of any change in the sequence of nucleic acid or any change in the chromosomal structure. Mutations can also be defined as heritable cha ...
The Gene Balance Hypothesis: From Classical Genetics to Modern
... www.plantcell.org/cgi/doi/10.1105/tpc.106.049338 ...
... www.plantcell.org/cgi/doi/10.1105/tpc.106.049338 ...
Nucleotide substitutions and evolution of duplicate genes.
... In a large-scale analysis involving several pairs of genes the sequences in one pair have a different length than sequences in another pair. Thus the goal is to compute the number of substitutions per site or number of substitutions per codon. In our search for duplicate genes we used two different ...
... In a large-scale analysis involving several pairs of genes the sequences in one pair have a different length than sequences in another pair. Thus the goal is to compute the number of substitutions per site or number of substitutions per codon. In our search for duplicate genes we used two different ...
Document
... signatures of motifs and domains Prosite consists of annotated sites/motifs/signatures/fingerprints Given an uncharacterized translated protein sequence, prosite tries to predict which motifs and domains make up the protein and thus identify the family to which it belongs ...
... signatures of motifs and domains Prosite consists of annotated sites/motifs/signatures/fingerprints Given an uncharacterized translated protein sequence, prosite tries to predict which motifs and domains make up the protein and thus identify the family to which it belongs ...
A phage library and two cosmid libraries were
... Two cosmid libraries were prepared according to different experimental protocols (Materials and Methods). For the construction of both libraries (I and II) Mspl partial digests of the same human placenta DNA were used. The insert of the M13 subclone 1-1 was used to screen both cosmid libraries. A to ...
... Two cosmid libraries were prepared according to different experimental protocols (Materials and Methods). For the construction of both libraries (I and II) Mspl partial digests of the same human placenta DNA were used. The insert of the M13 subclone 1-1 was used to screen both cosmid libraries. A to ...
Gene Prediction - Compgenomics2010
... Viterbi algorithm then calculates the functional sequence X* such that P(X*|S) is the largest among all possible values of X. ...
... Viterbi algorithm then calculates the functional sequence X* such that P(X*|S) is the largest among all possible values of X. ...
comparative genomics, minimal gene
... that it is, in fact, more appropriate to speak of a minimal set of essential functional niches (given specified conditions) rather than of minimal sets of genes. These functional niches differ in their evolutionary/structural redundancy (propensity for NOGD), and two or more distinct solutions have ...
... that it is, in fact, more appropriate to speak of a minimal set of essential functional niches (given specified conditions) rather than of minimal sets of genes. These functional niches differ in their evolutionary/structural redundancy (propensity for NOGD), and two or more distinct solutions have ...
Localized hypermutation and associated gene losses in legume
... one large clade of legumes (the IR loss clade, or IRLC) (Wojciechowski et al. 2004), some of which also show other rearrangements of gene order. Chloroplast genomes in the IRLC species are also notable for having significant amounts of repetitive DNA, something not usually seen in angiosperm cpDNA ( ...
... one large clade of legumes (the IR loss clade, or IRLC) (Wojciechowski et al. 2004), some of which also show other rearrangements of gene order. Chloroplast genomes in the IRLC species are also notable for having significant amounts of repetitive DNA, something not usually seen in angiosperm cpDNA ( ...
Identification of three MADS‐box genes expressed in sunflower
... homeotic genes, encoding the A, B and C functions, act alone or in combination to give rise to sepals, petals, stamens and carpels. Genes in the AG group include the C function homeotic genes, involved in stamen, and carpel development. Genes in both the DEF and the GLO groups comprise the B functio ...
... homeotic genes, encoding the A, B and C functions, act alone or in combination to give rise to sepals, petals, stamens and carpels. Genes in the AG group include the C function homeotic genes, involved in stamen, and carpel development. Genes in both the DEF and the GLO groups comprise the B functio ...
Nature Biotechnology, 21(4) - Weizmann Institute of Science
... deaminase12. Of major relevance is the recent discovery that dsRNA can trigger posttranscriptional gene silencing through a phenomenon called RNA interference13. This evolutionarily conserved process involves the excision of small interfering RNAs (siRNAs) from dsRNA precursors by a multidomain ribo ...
... deaminase12. Of major relevance is the recent discovery that dsRNA can trigger posttranscriptional gene silencing through a phenomenon called RNA interference13. This evolutionarily conserved process involves the excision of small interfering RNAs (siRNAs) from dsRNA precursors by a multidomain ribo ...
Functional second genes generated by retrotransposition of the X
... phenotype similar to Minute, are also caused by a quantitative de®ciency of rRNA genes. These phenotypes may re¯ect a reduced rate of protein synthesis resulting from insuf®ciency of ribosomal components in early development (11,12). Recently, heterozygous mutations of the human RPS19 gene were foun ...
... phenotype similar to Minute, are also caused by a quantitative de®ciency of rRNA genes. These phenotypes may re¯ect a reduced rate of protein synthesis resulting from insuf®ciency of ribosomal components in early development (11,12). Recently, heterozygous mutations of the human RPS19 gene were foun ...
DNA sequence of the control region of phage D108: the N
... infecting phage DNA is Inserted nonspecifically and without replication into the host chromosome. ...
... infecting phage DNA is Inserted nonspecifically and without replication into the host chromosome. ...
Presentation Slides
... isolate mutants through transposons or chemical mutagenesis Rapid determination of the molecular basis of disease mechanisms ...
... isolate mutants through transposons or chemical mutagenesis Rapid determination of the molecular basis of disease mechanisms ...
Applications of Genome Rearrangements
... chromosomes of the human, mouse and rat. Blocks have similar gene content and order. Note that the estimated number of genes in the X chromosome is 2000. ...
... chromosomes of the human, mouse and rat. Blocks have similar gene content and order. Note that the estimated number of genes in the X chromosome is 2000. ...
www.mbio.ncsu.edu
... for chrII. The percentage of P. haloplanktis genes in synteny groups with a selection of 34 complete bacterial genomes is represented by green bars for chrI and by blue bars for chrII. The closest organism is S. oneidensis. (B) Comparison of the gene content of Pseudoalteromonas haloplanktis, Shewan ...
... for chrII. The percentage of P. haloplanktis genes in synteny groups with a selection of 34 complete bacterial genomes is represented by green bars for chrI and by blue bars for chrII. The closest organism is S. oneidensis. (B) Comparison of the gene content of Pseudoalteromonas haloplanktis, Shewan ...
Gene finding: putting the parts together
... for instance, will have either a very low specificity or a very bad sensitivity, such that they will either predict a huge number of false positives (fake promoters) or a very small number of true promoters. The same is essentially true for splice site prediction: if looked at in isolation, splice s ...
... for instance, will have either a very low specificity or a very bad sensitivity, such that they will either predict a huge number of false positives (fake promoters) or a very small number of true promoters. The same is essentially true for splice site prediction: if looked at in isolation, splice s ...
1 - BioMed Central
... tools (Tgicl) [10] was used to cluster the zebra finch sequences with a minimum length of 100 bases and identity of 96% for overlapping regions into 9,716 consensus contigs. These zebra finch contigs were searched against the chicken protein sequences using Blastx [11], with an E value ≤ e-10 separa ...
... tools (Tgicl) [10] was used to cluster the zebra finch sequences with a minimum length of 100 bases and identity of 96% for overlapping regions into 9,716 consensus contigs. These zebra finch contigs were searched against the chicken protein sequences using Blastx [11], with an E value ≤ e-10 separa ...
Towards safer vectors for the field release of recombinant bacteria
... recombinant DNA release experiment. For example, the toluene degradation genes of P. putida, or the nitrogen fixation genes of Sinorhizobium meliloti, should have a lower risk potential for human health than those of the virulence genes of, for example Vibrio cholerae. Problems of this type have no ...
... recombinant DNA release experiment. For example, the toluene degradation genes of P. putida, or the nitrogen fixation genes of Sinorhizobium meliloti, should have a lower risk potential for human health than those of the virulence genes of, for example Vibrio cholerae. Problems of this type have no ...
Transposable element
A transposable element (TE or transposon) is a DNA sequence that can change its position within the genome, sometimes creating or reversing mutations and altering the cell's genome size. Transposition often results in duplication of the TE. Barbara McClintock's discovery of these jumping genes earned her a Nobel prize in 1983.TEs make up a large fraction of the C-value of eukaryotic cells. There are at least two classes of TEs: class I TEs generally function via reverse transcription, while class II TEs encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins. It has been shown that TEs are important in genome function and evolution. In Oxytricha, which has a unique genetic system, they play a critical role in development. They are also very useful to researchers as a means to alter DNA inside a living organism.