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Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run. mRIN [11] - Assessing mRNA integrity directly from RNA-Seq data.
An open reading frame (ORF) is a reading frame that has the potential to be transcribed into RNA and translated into protein. It requires a continuous sequence of DNA which may include a start codon, through a subsequent region which has a length that is a multiple of 3 nucleotides, to a stop codon in the same reading frame.
Ribosome moves along the mRNA template and nascent peptide is being made. When the ribosome reaches the 3’ end of the template, the fused puromycin will enter the A site of the ribosome. b. The mRNA-polypeptide fusion is released. All mRNA templates used for mRNA display technology have puromycin at their 3’ end.
These tools determine read counts from aligned RNA-Seq data, but alignment-free counts can also be obtained with Sailfish [87] and Kallisto. [88] The read counts are then converted into appropriate metrics for hypothesis testing, regressions, and other analyses. Parameters for this conversion are:
The ribosome facilitates decoding by inducing the binding of complementary transfer RNA (tRNA) anticodon sequences to mRNA codons. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is "read" by the ribosome. Translation proceeds in three phases:
The ORF Finder (Open Reading Frame Finder) [16] is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. This tool identifies all open reading frames using the standard or alternative genetic codes.
Ribosome profiling, or Ribo-Seq (also named ribosome footprinting), is an adaptation of a technique developed by Joan Steitz and Marilyn Kozak almost 50 years ago that Nicholas Ingolia and Jonathan Weissman adapted to work with next generation sequencing that uses specialized messenger RNA sequencing to determine which mRNAs are being actively translated.
In case of TCP-seq, ribosomes and ribosomal subunits engaged in interaction with mRNA are first fast chemically crosslinked to it with formaldehyde to preserve existing state of interactions (“snapshot” of distribution) and to block any possible non-equilibrium processes. The crosslinking can be performed directly in, but not restricted to ...
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