With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan （in the LaserGene package） is an excellent program with an easy-t...With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan （in the LaserGene package） is an excellent program with an easy-to-use graphical user interface （GUI） employed to assemble Sanger sequences into contigs. However, with increasing data size, larger sample sets and more sequenced loci make contig assemble complicated due to the considerable number of manual operations required to run SeqMan. Here, we present the ＇autoSeqMan＇ software program, which can automatedly assemble contigs using SeqMan scripting language. There are two main modules available, namely, ＇Classification＇ and ＇Assembly＇. Classification first undertakes preprocessing work, whereas Assembly generates a SeqMan script to consecutively assemble contigs for the classified files. Through comparison with manual operation, we showed that autoSeqMan saved substantial time in the preprocessing and assembly of Sanger sequences. We hope this tool will be useful for those with large sample sets to analyze, but with little programming experience. It is freely available at https：//github.com/ Sun-Yanbo/autoSeqMan.展开更多
We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa, Guang Lu Ai 4.An entire representative (sixfold coverage of rice chromosomes) and genetically stable BAC library of rice ...We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa, Guang Lu Ai 4.An entire representative (sixfold coverage of rice chromosomes) and genetically stable BAC library of rice genome constructed in this lab has been systematically analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. And all the images thus obtained were subject to image-processing, which consisted of preliminary location of bands, cooperative tracking of lanesby correlation of adjacent bands, a precise densitometric pass, alignment at the marker bands with the standard,optional interactive editing, and normalization of the accepted bands. The contigs were generated based on the Computer Software specially designed for genome map ping. The number of contigs with 600 kb in length on average was 464; of contigs with 1000 kb in length on average was 107; of contigs with 1500 kb in length on average was 23. Therefore, all the contigs we have obtained amounted up to 420 megabases in length. Considering the size of rice genome (430 megabased), the contigs generated in this lab have covered nearly 98% of the rice genome. We are now in the process of mapping the contigs to chromosomes.展开更多
The YAC contig construction has been done for the Human X chromosome short armXp21.3—p11.3, a region which contains several genetic disease gene loci and is of highlybiomedical importance. Using known probes(OTC, DXS...The YAC contig construction has been done for the Human X chromosome short armXp21.3—p11.3, a region which contains several genetic disease gene loci and is of highlybiomedical importance. Using known probes(OTC, DXS166, DMDcDNA) and STS markersof this region, YAC screenings are performed by both YAC colony in situ hybridization andPCR methods. Totally 55 YACs are obtained from the YAC libraries of CEPH, ICRF andthe Institute. The size determination, the analysis of 26 pairs of microsatelite STS, the single copy probe hybridization and the Alu-PCR fingerprinting are performed for these YACs.The mapping of these YACs is performed, and finally, 6 YAC contigs in Xp21.3—11.3 are obtained, covering about 15 Mb. This work will greatly facilitate the positional cloning of disease genes or the genome sequencing in this important region.展开更多
A major gene for heading date in rice, Ef(t), was mapped on the same position as one RFLP marker C1369 on chromosome 10, which was located between two RFLP markers C234 and G37 at 1.0 cM interval. Initially, these thr...A major gene for heading date in rice, Ef(t), was mapped on the same position as one RFLP marker C1369 on chromosome 10, which was located between two RFLP markers C234 and G37 at 1.0 cM interval. Initially, these three RFLP markers were used to screen a rice BAC library and seven independent clones with the size ranged from 70kb to 180kb were identified. By the comparisons of Hind III restriction fragment in each clone, the relative location of these clones were determined and two primary contigs, contig C1369 and contig G37, were obtained. Chromosome walking was performed with one outmost BAC end of the primary BAC contig C1369, then two contigs were integrated into one. The resultant contig encompassing Ef(t) gene locus which consisted of 7 BAC clones was developed. It will facilitate the isolation of Ef(t) gene using map based cloning approach.展开更多
In August 1992, the State S&T Commission(SSTC) of China announced that China would launch a Rice Genome Program, a counterpart to the US Program of Human Genome, in a bid to decipher the genetic code of rice at th...In August 1992, the State S&T Commission(SSTC) of China announced that China would launch a Rice Genome Program, a counterpart to the US Program of Human Genome, in a bid to decipher the genetic code of rice at the molecular level and then apply the obtained results to the cultivation of improved strains of the crop.展开更多
基金supported by the National Natural Science Foundation of China(31671326)the Youth Innovation Promotion Association,Chinese Academy of Sciences
文摘With the wide application of DNA sequencing technology, DNA sequences are still increasingly generated through the Sanger sequencing platform. SeqMan （in the LaserGene package） is an excellent program with an easy-to-use graphical user interface （GUI） employed to assemble Sanger sequences into contigs. However, with increasing data size, larger sample sets and more sequenced loci make contig assemble complicated due to the considerable number of manual operations required to run SeqMan. Here, we present the ＇autoSeqMan＇ software program, which can automatedly assemble contigs using SeqMan scripting language. There are two main modules available, namely, ＇Classification＇ and ＇Assembly＇. Classification first undertakes preprocessing work, whereas Assembly generates a SeqMan script to consecutively assemble contigs for the classified files. Through comparison with manual operation, we showed that autoSeqMan saved substantial time in the preprocessing and assembly of Sanger sequences. We hope this tool will be useful for those with large sample sets to analyze, but with little programming experience. It is freely available at https：//github.com/ Sun-Yanbo/autoSeqMan.
文摘We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa, Guang Lu Ai 4.An entire representative (sixfold coverage of rice chromosomes) and genetically stable BAC library of rice genome constructed in this lab has been systematically analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. And all the images thus obtained were subject to image-processing, which consisted of preliminary location of bands, cooperative tracking of lanesby correlation of adjacent bands, a precise densitometric pass, alignment at the marker bands with the standard,optional interactive editing, and normalization of the accepted bands. The contigs were generated based on the Computer Software specially designed for genome map ping. The number of contigs with 600 kb in length on average was 464; of contigs with 1000 kb in length on average was 107; of contigs with 1500 kb in length on average was 23. Therefore, all the contigs we have obtained amounted up to 420 megabases in length. Considering the size of rice genome (430 megabased), the contigs generated in this lab have covered nearly 98% of the rice genome. We are now in the process of mapping the contigs to chromosomes.
基金Supported by the High Technology Research and Development Programme of Chinathe National Natural Science Foundation of China
文摘The YAC contig construction has been done for the Human X chromosome short armXp21.3—p11.3, a region which contains several genetic disease gene loci and is of highlybiomedical importance. Using known probes(OTC, DXS166, DMDcDNA) and STS markersof this region, YAC screenings are performed by both YAC colony in situ hybridization andPCR methods. Totally 55 YACs are obtained from the YAC libraries of CEPH, ICRF andthe Institute. The size determination, the analysis of 26 pairs of microsatelite STS, the single copy probe hybridization and the Alu-PCR fingerprinting are performed for these YACs.The mapping of these YACs is performed, and finally, 6 YAC contigs in Xp21.3—11.3 are obtained, covering about 15 Mb. This work will greatly facilitate the positional cloning of disease genes or the genome sequencing in this important region.
文摘A major gene for heading date in rice, Ef(t), was mapped on the same position as one RFLP marker C1369 on chromosome 10, which was located between two RFLP markers C234 and G37 at 1.0 cM interval. Initially, these three RFLP markers were used to screen a rice BAC library and seven independent clones with the size ranged from 70kb to 180kb were identified. By the comparisons of Hind III restriction fragment in each clone, the relative location of these clones were determined and two primary contigs, contig C1369 and contig G37, were obtained. Chromosome walking was performed with one outmost BAC end of the primary BAC contig C1369, then two contigs were integrated into one. The resultant contig encompassing Ef(t) gene locus which consisted of 7 BAC clones was developed. It will facilitate the isolation of Ef(t) gene using map based cloning approach.
文摘In August 1992, the State S&T Commission(SSTC) of China announced that China would launch a Rice Genome Program, a counterpart to the US Program of Human Genome, in a bid to decipher the genetic code of rice at the molecular level and then apply the obtained results to the cultivation of improved strains of the crop.
