Letter Detecting Sequence Homology at the
... Background and Rationale Many biological systems and pathways, not only from bacteria, archaea, and fungi, but also from plants (Field and Osbourn 2008) and animals (Garcia-Fernandez 2005) are encoded by genes that are physically clustered together on the chromosome in operons or gene clusters (Fisc ...
... Background and Rationale Many biological systems and pathways, not only from bacteria, archaea, and fungi, but also from plants (Field and Osbourn 2008) and animals (Garcia-Fernandez 2005) are encoded by genes that are physically clustered together on the chromosome in operons or gene clusters (Fisc ...
Camelid Geneticists Chart Course for Future Research
... blocks” using “chromosome painting” and other technical jargon as casually as most of us talk about fleece weights and crimp styles. I am in awe! And my eyes are not glazing over. I am actually following most of it and learning so much – such as how traces are used to identify contigs, that are comb ...
... blocks” using “chromosome painting” and other technical jargon as casually as most of us talk about fleece weights and crimp styles. I am in awe! And my eyes are not glazing over. I am actually following most of it and learning so much – such as how traces are used to identify contigs, that are comb ...
Molecular markers closely linked to fusarium resistance genes in
... Fusarium oxysporum f.sp. ciceri races 4 and 5 was used to develop DNA amplification fingerprinting markers linked to both resistance loci. Bulked segregant analysis revealed 19 new markers on linkage group 2 of the genetic map on which the resistance genes are located. Closest linkage (2.0 cM) was o ...
... Fusarium oxysporum f.sp. ciceri races 4 and 5 was used to develop DNA amplification fingerprinting markers linked to both resistance loci. Bulked segregant analysis revealed 19 new markers on linkage group 2 of the genetic map on which the resistance genes are located. Closest linkage (2.0 cM) was o ...
The mutagenic chain reaction: A method for converting heterozygous
... It is often desirable to generate recessive loss-of-function (♂) X y+ female (♀) crosses and 7 F0♀ X y+♂ crosses we mutations in emergent model organisms, however, scoring recovered y- F1♀ progeny, which should not happen for such mutations in the heterozygous condition is according to Mendelian inh ...
... It is often desirable to generate recessive loss-of-function (♂) X y+ female (♀) crosses and 7 F0♀ X y+♂ crosses we mutations in emergent model organisms, however, scoring recovered y- F1♀ progeny, which should not happen for such mutations in the heterozygous condition is according to Mendelian inh ...
Access to the Maize Genome: An Integrated Physical and Genetic Map
... genes based on their function and/or their position in the genome; documenting all genes and their interplay; defining and exploring all the existing genetic diversity in a species; and using functional information and syntenic relationships of genes in closely related species to extrapolate gene fu ...
... genes based on their function and/or their position in the genome; documenting all genes and their interplay; defining and exploring all the existing genetic diversity in a species; and using functional information and syntenic relationships of genes in closely related species to extrapolate gene fu ...
Human Chromosomes and Genes
... animation that explains why: http://www.hhmi.org/biointeractive/gender/Y_evolution.html. ...
... animation that explains why: http://www.hhmi.org/biointeractive/gender/Y_evolution.html. ...
Close relationship between non-viral retroposons in Drosophila
... binding proteins derived from the cleavage of retroviral gag polyproteins. Functionally related polypeptides are similarly encoded by members of two other Drosophila repeated DNA families, the F elements and the I factors. The similarity in structural organization and the relatedness of their potent ...
... binding proteins derived from the cleavage of retroviral gag polyproteins. Functionally related polypeptides are similarly encoded by members of two other Drosophila repeated DNA families, the F elements and the I factors. The similarity in structural organization and the relatedness of their potent ...
Davies, Kelli: Eukaryotic Gene Prediction
... discovery. Once genes are identified, further analysis of the coding sequence can be used to identify protein domains to help illuminate function and determine candidates for further study. Homologs in different organisms can be identified via sequence alignment and then further studies can be condu ...
... discovery. Once genes are identified, further analysis of the coding sequence can be used to identify protein domains to help illuminate function and determine candidates for further study. Homologs in different organisms can be identified via sequence alignment and then further studies can be condu ...
Supplemental Figure and Methods
... variants, variants close to exon/intron boundaries, and variants in 8-species conserved regions (multiz8way) (27). We selected 122 additional non-synonymous and potential splice-site SNPs with dbSNP minor allele frequency (MAF) >.05 that were not present in HapMap. When HapMap release 21 became avai ...
... variants, variants close to exon/intron boundaries, and variants in 8-species conserved regions (multiz8way) (27). We selected 122 additional non-synonymous and potential splice-site SNPs with dbSNP minor allele frequency (MAF) >.05 that were not present in HapMap. When HapMap release 21 became avai ...
Ribosomal DNA sequences reveal gregarine pathogens
... The gene coding for the small subunit of ribosomal RNA (SSU RNA) is the most intensively sequenced marker for phylogenetic studies in all groups of organisms, including mites. Newly obtained sequence data can be quickly and easily compared with all published sequences of this marker deposited in Gen ...
... The gene coding for the small subunit of ribosomal RNA (SSU RNA) is the most intensively sequenced marker for phylogenetic studies in all groups of organisms, including mites. Newly obtained sequence data can be quickly and easily compared with all published sequences of this marker deposited in Gen ...
CalbiCyc, Metabolic Pathways at the Candida Genome Database
... Curation challenge: Steep learning curve for the curation tools. The tools are quite different, and the process is distinct, from the usual gene-centric curation we do, curators need to “switch gears” for pathway curation. Found that it was easier to make progress by making a focused “project” out o ...
... Curation challenge: Steep learning curve for the curation tools. The tools are quite different, and the process is distinct, from the usual gene-centric curation we do, curators need to “switch gears” for pathway curation. Found that it was easier to make progress by making a focused “project” out o ...
RNAi and RNAa - The Yin and Yang of RNAome
... was duly recognized and they were awarded with Nobel Prize for Physiology or Medicine in 2006 [3]. This gene knock down phenomenon was subsequently observed and experimentally proved in flies [4, 5. 6], and vertebrates [7, 8]. siRNAs theoretically represent ideal drugs for the specific inhibition of ...
... was duly recognized and they were awarded with Nobel Prize for Physiology or Medicine in 2006 [3]. This gene knock down phenomenon was subsequently observed and experimentally proved in flies [4, 5. 6], and vertebrates [7, 8]. siRNAs theoretically represent ideal drugs for the specific inhibition of ...
The Arabidopsis chloroplast ribosomal protein L21 is
... sequences of cytoplasmic 60S L21 r-proteins that possess a different signature than prokaryotic L21 r-proteins were not included in the trees. Only the Fitch–Margoliash tree is shown (Fig. 3). Results indicate that plant RPL21 r-proteins belong to two different clades. Similar results were obtained ...
... sequences of cytoplasmic 60S L21 r-proteins that possess a different signature than prokaryotic L21 r-proteins were not included in the trees. Only the Fitch–Margoliash tree is shown (Fig. 3). Results indicate that plant RPL21 r-proteins belong to two different clades. Similar results were obtained ...
The 2R hypothesis and the human genome sequence
... separate loci without actually causing the diploidisation of the chromosomes in question. The mammalian Y chromosome may serve as a model for this process. It is an unusual chromosome because it is partially diploid (at the pseudoautosomal region), and the rest is haploid. Lahn and Page (1999) ident ...
... separate loci without actually causing the diploidisation of the chromosomes in question. The mammalian Y chromosome may serve as a model for this process. It is an unusual chromosome because it is partially diploid (at the pseudoautosomal region), and the rest is haploid. Lahn and Page (1999) ident ...
2009 Hart and Grosbe.. - Evolution and Ecology | UC Davis
... molecular mechanisms of adaptive phenotypic evolution. An incisive test of Williamson’s specific prediction (6) will depend on the results of a whole-genome sequence analysis of a velvet worm. The best available evidence comes from molecular phylogenetic analyses, which Williamson’s hypothesis predi ...
... molecular mechanisms of adaptive phenotypic evolution. An incisive test of Williamson’s specific prediction (6) will depend on the results of a whole-genome sequence analysis of a velvet worm. The best available evidence comes from molecular phylogenetic analyses, which Williamson’s hypothesis predi ...
Repeat mediated gene duplication in the Drosophila
... was added, and this longer sequence was used to identify the endpoints (via BLAST). This process was repeated until the alignment no longer terminated at the end of the partition, and the duplication endpoint was identified. Protein coding sequences were inferred using the initial published annotatio ...
... was added, and this longer sequence was used to identify the endpoints (via BLAST). This process was repeated until the alignment no longer terminated at the end of the partition, and the duplication endpoint was identified. Protein coding sequences were inferred using the initial published annotatio ...
The evolutionary history of the stearoyl
... genome [21]. As a consequence, numerous gene families have specifically expanded up to four copies in the vertebrate lineage. An extra genome duplication in teleosts (3R) [22] contributed further to gene number increase. With respect to the SCD gene family, while the two SCD1 teleost isoforms have c ...
... genome [21]. As a consequence, numerous gene families have specifically expanded up to four copies in the vertebrate lineage. An extra genome duplication in teleosts (3R) [22] contributed further to gene number increase. With respect to the SCD gene family, while the two SCD1 teleost isoforms have c ...
Name that Gene Project The National Center for Biotechnology
... EXERCISE 1: From the main BLAST page select Nucleotide BLAST. This brings up a web page where you can specify your query sequence along with various parameters. Copy and paste the above "dinosaur DNA" sequence into the window labeled Enter Query Sequence, and then click the BLAST button at the botto ...
... EXERCISE 1: From the main BLAST page select Nucleotide BLAST. This brings up a web page where you can specify your query sequence along with various parameters. Copy and paste the above "dinosaur DNA" sequence into the window labeled Enter Query Sequence, and then click the BLAST button at the botto ...
pdf
... regions to consider, with 51 unique flanking genes. There are 6 super-regions with at least 99 bp overlapping with ultra-conserved elements. At least one of the flanking genes for each of these 6 super-regions is a transcription factor located 1–314 kb away (IRX3, IRX5, IRX6, HOXD13, DMRT1, DMRT3, F ...
... regions to consider, with 51 unique flanking genes. There are 6 super-regions with at least 99 bp overlapping with ultra-conserved elements. At least one of the flanking genes for each of these 6 super-regions is a transcription factor located 1–314 kb away (IRX3, IRX5, IRX6, HOXD13, DMRT1, DMRT3, F ...
Real Time PCR Testing for Biotech Crops: Issues
... events are results of single insertion in a given region of genome, thereby resulting in a unique signature site for each transgenes. Results are not influence by copy number of promoter/terminator sequence or copy of transgenes. ...
... events are results of single insertion in a given region of genome, thereby resulting in a unique signature site for each transgenes. Results are not influence by copy number of promoter/terminator sequence or copy of transgenes. ...
Guidelines for Genetic Nomenclature and Community Governance
... may be made at intervals to accommodate changing needs. Individuals who wish to propose changes to the guidelines should circulate the amendments to members of the research community and post the proposed changes at the M. truncatula forum on the World Wide Web (http://www.medicago.org). Proposals t ...
... may be made at intervals to accommodate changing needs. Individuals who wish to propose changes to the guidelines should circulate the amendments to members of the research community and post the proposed changes at the M. truncatula forum on the World Wide Web (http://www.medicago.org). Proposals t ...
Catalyzing Bacterial Speciation: Correlating Lateral Transfer with
... malate dehydrogenases, and vice versa. Because analyses of proteins families demonstrate that enzymatic novelties have arisen very few times, the distribution of these enzymes among extant organisms— including both Bacteria and Archaea—must reect one of two processes. Either genes encoding all enzy ...
... malate dehydrogenases, and vice versa. Because analyses of proteins families demonstrate that enzymatic novelties have arisen very few times, the distribution of these enzymes among extant organisms— including both Bacteria and Archaea—must reect one of two processes. Either genes encoding all enzy ...
Expansion of specialized metabolism
... evolutionary scenario of the diversification of specialized metabolism gene by the whole genome duplication (WGD) and local tandem duplication (LTD) is presented. Arrows indicate the hypothetical specialized metabolism genes on chromosomes of ancestral and extant plant. In this hypothetical scenario ...
... evolutionary scenario of the diversification of specialized metabolism gene by the whole genome duplication (WGD) and local tandem duplication (LTD) is presented. Arrows indicate the hypothetical specialized metabolism genes on chromosomes of ancestral and extant plant. In this hypothetical scenario ...
Missing Value Estimation for Gene Expression Profile Data
... of the observed values over that gene[5] . Case deletion procedures may bias the results if the remaining cases are unrepresentative of the entire sample. Because the same value is used to replace MVs in a given gene, both zero and mean substitutions will reduce the variance of the variable in quest ...
... of the observed values over that gene[5] . Case deletion procedures may bias the results if the remaining cases are unrepresentative of the entire sample. Because the same value is used to replace MVs in a given gene, both zero and mean substitutions will reduce the variance of the variable in quest ...
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.