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Clc sequence viewer sanger12/23/2023 Genomics: whole genome re-sequencing and targeted re-sequencing of genomes of any size and type, de novo assembly of an unlimited number of reads, SNP and DIP detection, identification of genomic rearrangements.Other bioinformatics features: multiple alignment of DNA, RNA, and proteins, sequence editor, local complexity region analysesĬLC Genomics Workbench is a cross-platform desktop application that incorporates cutting-edge technology and algorithms for analyzing and visualizing next generation sequencing data.Project and data management: detailed history log, full integration of data input, data management, calculation results, and data export Database searches: GenBank Entrez, BLAST on local databases, PubMed.Pattern search: motif searches for basic patterns, using regular expressions, and/or with ProSite patterns.Protein sequence analysis: antigenicity, PFAM domain search, transmembrane helix prediction, proteolytic cleavage detection RNA structure analysis: secondary structure prediction, symbolic representations.DNA sequence analysis: primer design, in silico PCR, cloning, SNP annotation, restriction enzyme analysis and management.Expression analysis including digital gene expression: support for both microarray and sequencing-based expression data, clustering algorithms, tools for Gene Set Enrichment Analysis.Noteworthy features include but are not limited to: CLC Main Workbench supports researcher’s daily bioinformatics needs and CLC Genomics Workbench handles sequencing data from high-throughput sequencing systems.ĬLC Main Workbench is an integrated software package that enables users to perform advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, seamless data management, and user-friendly graphical viewing and output options. Since I can detect mRNA, I was wondering if it’s possible that my construct gets transcribed (although probably with an extensive 3’ UTR) but can’t be properly/efficiently translated due to the lack of PolyA signal.The HSLS Molecular Biology Information Service recently licensed two new bioinformatics resources from CLC bio. I sequenced the whole plasmid that I used for recombination as well DNA from the cells after recombination and the sequences seem to be completely correct. I also performed a functional test, from which it was clear that I don’t have any functional protein in the recombined cells. However, when I performed IF with the antibody that I know works (it worked for the positive control) I couldn’t detect my protein. I could indeed detect mRNA expression by qPCR (there was a significant difference between wt (non-recombined cells), -dox and +dox conditions Cts for +dox were still relatively high though). After recombination of this cassette into the genome of the cells that already express rtTA and culturing in the presence of dox, I was hoping to see the expression of my gene of interest. ![]() On this construct I have a Tet-dependant promoter that I know works and my gene of interest downstream of it, but there is no polyA signal. The reason why I’m asking this is because I work with the construct that is used for transgenesis through recombination. I’m wondering if lack of such signal can lead to the complete absence of the protein expression. It is my understanding that polyA signal isn’t absolutely necessary for mammalian gene expression but it’s highly recommended to use it whenever possible.
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