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4 materials found

Keywords: Scoring matrices  or Best Practices  or Sequence Analysis  or Interpro 

and

Authors: Obi Griffith  or blankclemens  or Martin Morgan  or Bruno Gaeta  or Yo Yehudi 


Best Practices for Managing R / Bioconductor Scripts

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Best Practices

Best Practices for Managing R / Bioconductor Scripts https://tess.elixir-europe.org/materials/best-practices-for-managing-r-bioconductor-scripts Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Best Practices
Introduction to Bioconductor for Sequence Analysis

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an...

Keywords: Sequence Analysis

Introduction to Bioconductor for Sequence Analysis https://tess.elixir-europe.org/materials/introduction-to-bioconductor-for-sequence-analysis Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images. Sequence Analysis
Similarity searching, multiple sequence alignment and protein families - undergraduate lab

Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of...

Keywords: Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching

Similarity searching, multiple sequence alignment and protein families - undergraduate lab https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of the exercises make use of public databases they need to be checked and in some cases updated every time the lab is run. The lab is meant to be easily assessed using an online quiz (I use moodle). I provides a hands on introduction to NCBI BLAST, Interproscan, Clustal, MUSCLE and T-COFFEE, and HMMER.  Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching biology and bioinformatics sophomore undergraduates 2013-11-12 2017-10-09
Sequence comparison - undergraduate lab

This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of...

Keywords: Dotmatrix plots, Scoring matrices, Sequence alignment

Sequence comparison - undergraduate lab https://tess.elixir-europe.org/materials/sequence-comparison-undergraduate-lab This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of the lab should be easy to adapt to other environments. This lab makes use of EMBOSS programs, prss in the FASTA package, as well as the NCBI BLAST website. I usually deliver this lab after a series of lectures discussing dotmatrix plots and sequence alignment. Students enter their answers to the questions into a quiz set up within moodle which allows for easier marking. Dotmatrix plots, Scoring matrices, Sequence alignment Undergraduate students 2013-11-12 2017-10-09