![]() ![]() It can also be employed as a very useful teacher's assistant, as it allows one to view detailed, and informative base traces graphs. The application can receive samples from various sources, including ABI documents or Chromatogram files assembly projects can also be loaded and one can even extract data from a valid Genbank ID. Once loaded, users can perform a wide variety of actions upon source samples. Assemble sequences with cDNA to genomic algorithmsįor example, one can assemble sequences using multiple algorithms or remove base ambiguities using automated editing tools. Professional users will also appreciate the program's ability to show the protein translation for every sequence, as well as the mutation detection and analysis feature. The latter option displays informative charts based on sensitive SNP detection. This is based on heterozygous insertions or deletions analysis algorithms that target both secondary and primary peaks. Once satisfied with their projects, users can export their samples to FASTA files. Other options are available, including transferring assemblies, or consensus sequences, as well as protein translations and features. The application allows users to perform DNA sequencing analysis, complete with mutations detectionĪll things considered, CodonCode Aligner is a valuable tool for anyone involved in DNA sequencing and analysis. From simple sequence editing or trimming to complex mapping and phylogenetic tree operations, the program can be a highly useful research tool.Mosquitoes are the potential vectors for a variety of viruses that can cause diseases in the human and animal populations. Viruses in the order Picornavirales infect a broad range of hosts, including mosquitoes. In this study, we aimed to characterize a novel picorna-like virus from the Culex spp. of mosquitoes from the Zambezi Valley of Mozambique. ![]() The extracted RNA from mosquito pools was pre-amplified with the sequence independent single primer amplification (SISPA) method and subjected to high-throughput sequencing using the Ion Torrent platform. Reads that are classified as Iflaviridae, Picornaviridae and Dicistroviridae were assembled by CodonCode Aligner and SPAdes. Gaps between the viral contigs were sequenced by PCR. The genomic ends were analyzed by 5′ and 3′ RACE PCRs. The ORF was predicted with the NCBI ORF finder. The conserved domains were identified with ClustalW multiple sequence alignment, and a phylogenetic tree was built with MEGA. The presence of the virus in individual mosquito pools was detected by RT-PCR assay. ResultsĪ near full-length viral genome (9740 nt) was obtained in Culex mosquitoes that encoded a complete ORF (3112 aa), named Culex picorna-like virus (CuPV-1). The predicted ORF had 38% similarity to the Hubei picorna-like virus 35. The sequence of the conserved domains, Helicase-Protease-RNA-dependent RNA polymerase, were identified by multiple sequence alignment and found to be at the 3′ end, similar to iflaviruses. Phylogenetic analysis of the putative RdRP amino acid sequences indicated that the virus clustered with members of the Iflaviridae family. ![]() CuPV-1 was detected in both Culex and Mansonia individual pools with low infection rates. ![]() The study reported a highly divergent, near full-length picorna-like virus genome from Culex spp. The discovery and characterization of novel viruses in mosquitoes is an initial step, which will provide insights into mosquito-virus interaction mechanisms, genetic diversity and evolution. Viruses in the order Picornavirales infect a variety of plants, animal hosts and insects. The order consists of five viral families, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Secoviridae, and an unassigned group. Viruses in this order have a single-stranded, positive-sense RNA genome (+ssRNA) of approximately 9 KB in length and are non-enveloped. Most of the genomes in this order have a single open reading frame (ORF) that is flanked with a genome-linked, virus-encoded protein (VPg) at the 5′ end and a poly (A) tail at the 3′ end. ![]()
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