Supplementary Methods S2: Exome Sequencing
... (3) Aggregation of lane- and library-level data Multiple lanes and libraries are aggregated into a single BAM per sample. Lane‐ level BAM files are combined to library‐ level BAM files and these are then combined to sample-level BAM files. The BAM files contain read groups that represent the library ...
... (3) Aggregation of lane- and library-level data Multiple lanes and libraries are aggregated into a single BAM per sample. Lane‐ level BAM files are combined to library‐ level BAM files and these are then combined to sample-level BAM files. The BAM files contain read groups that represent the library ...
Supplement: Sequence analysis of GMR-dRetMEN2B
... AE003683 maps to different sites within AE003683. There may be 2 inserts, one in 1st intron of Dh, the other 92 bp upstream of Crc, or a single P that induced a 10.4 kb deletion to remove Scm, SpdS, the 1st exon of Dh ...
... AE003683 maps to different sites within AE003683. There may be 2 inserts, one in 1st intron of Dh, the other 92 bp upstream of Crc, or a single P that induced a 10.4 kb deletion to remove Scm, SpdS, the 1st exon of Dh ...
RefGen_v3_status_20120522
... submission of RefGen_v2, currently in use throughout the community, is illustrative of this problem. While this submission is still in process, feedback from validation has so far included i) contamination of sequence from non-maize organisms; ii) inappropriate gap placement and length representati ...
... submission of RefGen_v2, currently in use throughout the community, is illustrative of this problem. While this submission is still in process, feedback from validation has so far included i) contamination of sequence from non-maize organisms; ii) inappropriate gap placement and length representati ...
Tracing the origin of our species through palaeogenomics
... this case the one of present-day humans, since a de novo assemblage of an ancient genome based on these short molecules is not possible. The sequences may contain mistakes due to the damages that occur in DNA over time, therefore a higher coverage is required. Ideally each base should be sequenced a ...
... this case the one of present-day humans, since a de novo assemblage of an ancient genome based on these short molecules is not possible. The sequences may contain mistakes due to the damages that occur in DNA over time, therefore a higher coverage is required. Ideally each base should be sequenced a ...
Camelid Geneticists Chart Course for Future Research
... used in cattle may be applied to alpacas and other camelids. Reproductive anatomic and physiological traits are known to be controlled by genetics. Unfortunately, there are several anatomic and physiologic (hormonal) defects that interfere with the reproductive process and prevent optimal birthing o ...
... used in cattle may be applied to alpacas and other camelids. Reproductive anatomic and physiological traits are known to be controlled by genetics. Unfortunately, there are several anatomic and physiologic (hormonal) defects that interfere with the reproductive process and prevent optimal birthing o ...
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 ...
Characteristic Features of the Nucleotide Sequences of Yeast
... structural constraints within various regions of proteins encoded by respective genes are also conceivable factors affecting the statistical biases mentioned above. Based on these considerations, we investigated whether or not the mitochondrial ribosomal protein (MRP) genes of the budding yeast Sacc ...
... structural constraints within various regions of proteins encoded by respective genes are also conceivable factors affecting the statistical biases mentioned above. Based on these considerations, we investigated whether or not the mitochondrial ribosomal protein (MRP) genes of the budding yeast Sacc ...
(2) in ppt - NYU Computer Science
... • Consider a genomic location L and two “similar” nucleotide sequences sL,x and sL,y starting at that location in the two copies of a diploid genomes… – E.g., they may differ in one SNP. – Let qx and qy be their respective copy numbers in the whole genome and all copies are selected in the reduced c ...
... • Consider a genomic location L and two “similar” nucleotide sequences sL,x and sL,y starting at that location in the two copies of a diploid genomes… – E.g., they may differ in one SNP. – Let qx and qy be their respective copy numbers in the whole genome and all copies are selected in the reduced c ...
Precise insertion and guided editing of higher plant
... off target sites within the rice genome, both of which contained a 4 bp mismatch. Both genomic regions were amplified via PCR from multiple GE0001 events as well as from wild type rice. These fragments were subcloned, sequenced via Sanger sequencing and compared to the wild type sequences. No off-ta ...
... off target sites within the rice genome, both of which contained a 4 bp mismatch. Both genomic regions were amplified via PCR from multiple GE0001 events as well as from wild type rice. These fragments were subcloned, sequenced via Sanger sequencing and compared to the wild type sequences. No off-ta ...
SEGMENTAL VARIATION
... Regions that are deleted or duplicated should yield lesser or greater numbers of reads •Detection of breakpoints by: –Short paired reads (like Illumina paired-end sequencing) Are the sequences at two ends of a fragment both from the same chromosome? Are they the right distance apart? –Long reads (kb ...
... Regions that are deleted or duplicated should yield lesser or greater numbers of reads •Detection of breakpoints by: –Short paired reads (like Illumina paired-end sequencing) Are the sequences at two ends of a fragment both from the same chromosome? Are they the right distance apart? –Long reads (kb ...
mitochondrial mixing facilitated the evolution of sex at the
... between mitochondrial symbionts and the host. Evolution of complex life can be conceptualized as a sequence of major evolutionary transitions (Buss, 1987; Maynard Smith and Szathmary, 1995). With each transition conflicts between the levels of individuality arise and have to be mediated for a stable ...
... between mitochondrial symbionts and the host. Evolution of complex life can be conceptualized as a sequence of major evolutionary transitions (Buss, 1987; Maynard Smith and Szathmary, 1995). With each transition conflicts between the levels of individuality arise and have to be mediated for a stable ...
Foundations of Biology
... their genetic information to the nucleus. The hydrogenosome, a structure involved in carbohydrate metabolism found in some Archezoans (Muller, 1992), is now thought to represent a mitochondria that has lost its genetic information completely and along with that loss, the ability to do the Krebs cycl ...
... their genetic information to the nucleus. The hydrogenosome, a structure involved in carbohydrate metabolism found in some Archezoans (Muller, 1992), is now thought to represent a mitochondria that has lost its genetic information completely and along with that loss, the ability to do the Krebs cycl ...
Supporting Information (SI) for “Theoretical models of the influence
... Fig. S3. Effective migration rates over time for nine combinations of gross migration rates (m) and the average, per-locus strength of divergent selection (s) for large populations (N = 20,000). For reference, data from Fig. 1A,B,C in the main text are shown here as panels C, E, and I, respectively ...
... Fig. S3. Effective migration rates over time for nine combinations of gross migration rates (m) and the average, per-locus strength of divergent selection (s) for large populations (N = 20,000). For reference, data from Fig. 1A,B,C in the main text are shown here as panels C, E, and I, respectively ...
Bioinfo primer - part 6/6
... isolates. cDNA libraries are specific for tissue, developmental time, stimulation etc. – Therefore, looking at cDNA is looking at mRNA is looking at active genes. – To look at cDNA means sequencing (part of) it. • Clones are picked at random (10’000-200’000) • Sequenced from one or both ends once (n ...
... isolates. cDNA libraries are specific for tissue, developmental time, stimulation etc. – Therefore, looking at cDNA is looking at mRNA is looking at active genes. – To look at cDNA means sequencing (part of) it. • Clones are picked at random (10’000-200’000) • Sequenced from one or both ends once (n ...
GCAT-SEEK Workshop - Prokaryotic Genomics Module – Jeff
... A journey of a thousand miles begins with one step (Chinese philosopher, Lao-tzu). The isolation of genomic DNA from most bacteria is rather straightforward, and there are several kits available from different manufacturers. We typically use the Qiagen Blood and Tissue Kit because the kit can be use ...
... A journey of a thousand miles begins with one step (Chinese philosopher, Lao-tzu). The isolation of genomic DNA from most bacteria is rather straightforward, and there are several kits available from different manufacturers. We typically use the Qiagen Blood and Tissue Kit because the kit can be use ...
Genome Evolution in an Insect Cell: Distinct
... symbiont the most AT-rich bacterial genome yet characterized (Clark et al., 2001). Analysis of six kilobases of Blochmannia sequences (unpubl. data) corroborates earlier evidence of low GC content for this bacterial genome (⬃30% GC; Dasch, 1975). This AT bias has a strong impact on the amino acid co ...
... symbiont the most AT-rich bacterial genome yet characterized (Clark et al., 2001). Analysis of six kilobases of Blochmannia sequences (unpubl. data) corroborates earlier evidence of low GC content for this bacterial genome (⬃30% GC; Dasch, 1975). This AT bias has a strong impact on the amino acid co ...
Practice exam
... adulthood. Squares represent males and circles females. Roman numerals indicate generations and Arabic numerals indicate individuals. 1a [5 pt] List two features of the inheritance pattern for vision loss that are consistent with vision loss due to a mitochondrial mutation. ...
... adulthood. Squares represent males and circles females. Roman numerals indicate generations and Arabic numerals indicate individuals. 1a [5 pt] List two features of the inheritance pattern for vision loss that are consistent with vision loss due to a mitochondrial mutation. ...
No Slide Title
... # of SLAM human/mouse genes # of SLAM human/rat genes # of SLAM genes identical in human, mouse, and rat # of SLAM human/mouse/rat genes overlapping human RefSeq % of SLAM human/mouse/rat genes with correct structure (out of genes overlapping human RefSeq) # of novel (not overlapping with human Ense ...
... # of SLAM human/mouse genes # of SLAM human/rat genes # of SLAM genes identical in human, mouse, and rat # of SLAM human/mouse/rat genes overlapping human RefSeq % of SLAM human/mouse/rat genes with correct structure (out of genes overlapping human RefSeq) # of novel (not overlapping with human Ense ...
Foundations of Biology - Geoscience Research Institute
... genes in amitochondrial eukaryotes all reinterpreted prevailing theory in saying that mitochondria must have been present then lost after they had transferred some of their genetic information to the nucleus. The hydrogenosome, a structure involved in carbohydrate metabolism found in some Archaezoan ...
... genes in amitochondrial eukaryotes all reinterpreted prevailing theory in saying that mitochondria must have been present then lost after they had transferred some of their genetic information to the nucleus. The hydrogenosome, a structure involved in carbohydrate metabolism found in some Archaezoan ...
Shotgun DNA sequencing using cloned DNase I
... 10-12], insertions greater than 350 bp in length are desirable in order to take full advantage of the resolving power of DNA sequencing gels. ...
... 10-12], insertions greater than 350 bp in length are desirable in order to take full advantage of the resolving power of DNA sequencing gels. ...
Slide 1
... 2. Why is the fate of most duplicate genes to rates, compared to angiosperms? Or, on eventually become silenced? Could the other hand, could the silenced genes mutations accumulate in both copies at the hold the key to the long history of fern same rate causing subfunctionalization, evolution? where ...
... 2. Why is the fate of most duplicate genes to rates, compared to angiosperms? Or, on eventually become silenced? Could the other hand, could the silenced genes mutations accumulate in both copies at the hold the key to the long history of fern same rate causing subfunctionalization, evolution? where ...
Kelly PD, Chu F, Woods IG, Ngo‑Hazelett P, Cardozo T, Huang H
... rodent cells. As such, markers that tend to be present in the same hybrid cell lines are closer together than those that are coretained infrequently. One limitation of this approach is that RH maps tend to have more uncertainty in the order of closely spaced markers than genetic maps, but an importa ...
... rodent cells. As such, markers that tend to be present in the same hybrid cell lines are closer together than those that are coretained infrequently. One limitation of this approach is that RH maps tend to have more uncertainty in the order of closely spaced markers than genetic maps, but an importa ...
The Complete Chloroplast and Mitochondrial DNA Sequence of
... clear similarity to other known genes. The compactness of the O. tauri mt genome is further illustrated by the shortness of the intergenic regions, ranging from 1 to 475 bp, with an average of 42 bp. Only 5 intergenic regions exceed 100 bp, and these are all located in the duplicated region. In addi ...
... clear similarity to other known genes. The compactness of the O. tauri mt genome is further illustrated by the shortness of the intergenic regions, ranging from 1 to 475 bp, with an average of 42 bp. Only 5 intergenic regions exceed 100 bp, and these are all located in the duplicated region. In addi ...
The Mitochondrial Genome of Chara vulgaris
... Département de Biochimie et de Microbiologie, Université Laval, Québec, Québec G1K 7P4, Canada ...
... Département de Biochimie et de Microbiologie, Université Laval, Québec, Québec G1K 7P4, Canada ...