ABSTRACT
<p><b>OBJECTIVE</b>To perform variation and phylogenetics analysis on the SARS-CoV genome sequence (PUMC01) isolated in the Peking Union Medical College Hospital.</p><p><b>METHODS</b>The cDNA library of SARS-CoV (PUMC01 isolate) was constructed by means of random-priming strategy. Random selected plasmid was sequenced and the genome sequence of SARS-CoV-PUMC01 was assembled by conventional methods (The Genebank Accession No. of SARS-CoV-PUMC01 is AY350750). The variation and phylogenetics analysis were performed by comparing the PUMC01 sequence with other SARS-CoV isolates.</p><p><b>RESULTS</b>Ten variation sites were found by comparing PUMC01 isolate with Tor2 and Urbani isolates. In phylogenetic analysis of 18 SARS-CoV isolates, two classes were observed and there is different differential time between these two classes and the different isolates in each class.</p><p><b>CONCLUSIONS</b>The evidence of phylogenetic analysis of different SARS-CoV isolates from different region is instructive for understanding the clinical relations between the different isolates and the transmission chain of SARS-CoV.</p>
Subject(s)
Amino Acid Sequence , Base Sequence , China , DNA, Viral , Genetics , Genetic Variation , Genome, Viral , Molecular Sequence Data , Phylogeny , Severe acute respiratory syndrome-related coronavirus , Genetics , Sequence Analysis, DNA , Viral Proteins , GeneticsABSTRACT
<p><b>OBJECTIVE</b>To annotate the human genome 3p24-p25 478 kb complete sequence.</p><p><b>METHODS</b>The protein-coding genes in the genomic sequence were identified by using ab initio gene finding, homology-based similarity database searching and all or partial mRNA aligning with genomic sequence, and the content feature of the genomic sequence were analyzed by using EMBOSS package.</p><p><b>RESULTS</b>Two known genes SLC6A1 and SLC6A11 were identified; as well as the GC content of this genomic sequence was 47% and 3 putative CpG islands were predicted in the genomic sequence, located in 130,685-131,516 bp, 307,090-307,870 bp and 415,585-416,308 bp, respectively.</p><p><b>CONCLUSIONS</b>The methods, as mentioned above, might be used for annotating the biological information in the genomic sequence, such as gene structure, GC content, CpG island.</p>