Kindlund E, Rubin CJ, Stromstedt L, Andersson B, Andersson L (2007). "A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms." Nature 432(7018): 717-22 Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Kindlund E International Chicken Polymorphism Map Consortium et. "GRAT-genome-scale rapid alignment tool." Comput Methods Programs Biomed Feb 8: Epub ahead of print Kindlund E, Tammi MT, Arner E, Nilsson D, Andersson B (2007). "Correcting errors in shotgun sequences." Nucleic Acids Res 31(15): 4663-72 Tammi MT, Arner E, Kindlund E, Andersson B (2003). Sequence alignment methods we have developed, and have provided important The genome analysis studies described in this thesis validated the DNA Of the annotated genes and found the gene content of T. Surface antigen genes and housekeeping genes. Genes are often repeated in tandem arrays, including Has interesting biological features, including a genome structure with Trypanosoma cruzi is a protozoan parasite which causes Chagas disease. The results showĮxtensive copy number variation, in some cases unique to domestic Genome hybridizations of different chicken breeds. Structural variation in the chicken genome through array comparative These findings indicate substantial sequenceĬopy number variation is emerging as an important source of genotypic and The results showed no evidence of large,ĭomestic-specific sweeps. Used this data to find signs of selective sweeps between wild andĭomestic chickens by searching for regions with low diversity withinĭomestic breeds. Sequences from three domesticĬhicken breeds were available for comparison to the genome sequence. Genetic factors involved in domestication. The genome sequencing of the wildĪncestor of domestic chickens have offered an opportunity to study The chicken is both an important agricultural source of protein and model At the same time, sequencing errors and polymorphismsīetween the sequences do not reduce sensitivity. Long seeds, which results in high specificity in the seeding and a fasterĪlignment program. Approximate seed matching allows the use of Matching algorithm which reduces the impact of this tradeoff by allowing Seeds are more likely to omit true alignments in the presence of Is a tradeoff between sensitivity and specificity in the seeding process,Īs short seeds are inefficient in eliminating spurious matches and long (seeds) are used to locate potential alignments that are verified. Most alignment programs use a seed and extend method, where subsequences This publication also describes the result from these projects. Methods in chicken and Trypanosoma cruzi genome analysis projects, and Sequence alignment that address these problems. This thesis describes new methods which we have developed for DNA Repeat sequences also make the analysis difficult. DNA sequence alignment is one of the most common bioinformatics tasks.Īlignment analysis for eukaryotic genomes is challenging because theĭatasets are large.
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