Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap (Q42696895)

5 November 2017

Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap (English)

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5 November 2017

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Aristeidis G Telonis

2

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Isidore Rigoutsos

object named as

Isidore Rigoutsos

series ordinal

3

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author name string

Phillipe Loher

series ordinal

1

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PubMed ID

29030853

5 November 2017

language of work or name

English

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publication date

1 January 2018

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Methods in Molecular Biology

5 November 2017

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5 November 2017

1680

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5 November 2017

237-255

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tRNA biology charges to the front

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tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins

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tRNA fragments in human health and disease

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Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies

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From tRNA to miRNA: RNA-folding contributes to correct entry into noncoding RNA pathways

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Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement

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A tRNA-derived fragment competes with mRNA for ribosome binding and regulates translation during stress.

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Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants.

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A comprehensive repertoire of tRNA-derived fragments in prostate cancer.

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Consequential considerations when mapping tRNA fragments

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Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges

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MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.

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Nuclear and mitochondrial tRNA-lookalikes in the human genome

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CCA addition to tRNA: implications for tRNA quality control

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tRNAHis-guanylyltransferase establishes tRNAHis identity

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3'-5' tRNAHis guanylyltransferase in bacteria

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Improved tools for biological sequence comparison

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Basic local alignment search tool

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Combined use of sequence similarity and codon bias for coding region identification

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BLAT—The BLAST-Like Alignment Tool

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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Fast and accurate short read alignment with Burrows-Wheeler transform

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BFAST: an alignment tool for large scale genome resequencing

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SHRiMP2: sensitive yet practical SHort Read Mapping

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GtRNAdb: a database of transfer RNA genes detected in genomic sequence

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Cutadapt removes adapter sequences from high-throughput sequencing reads

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Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells

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GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

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Life without post-transcriptional addition of G-1: two alternatives for tRNAHis identity in Eukarya

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MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments.

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tRFdb: a database for transfer RNA fragments

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tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers.

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ViennaRNA Package 2.0

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10.1007/978-1-4939-7339-2_16

21 January 2018

Identifiers

DOI

1 reference

5 November 2017

1 reference

PubMed ID

29030853