Michael Grünstäudl (Gruenstaeudl), PhD

Researcher at the Freie Universität Berlin

Monatsarchiv für September 2015

Correcting tRNA annotations

How to call the anticodon? Over the past few days I have been correcting genomic annotations using custom bash and Python code. One of the more interesting exercises has been the homogenization of the „product“ tags for transfer RNAs, which provide information about the respective anticodon sequences. In the majority of databases familiar to me, […]

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Displaying phylogeny over map

A brief, preliminary evaluation For the revision of a new manuscript, I needed to generate a figure, in which a phylogenetic tree is plotted over a geographic map. The tips of the tree shall hereby point to the distribution area of the taxa they represent on the underlying map. Lucky for me, Rod Page has […]

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Trees Nex2Phy one-liner

Tree file format conversion for the efficient Today, I needed to convert a series of phylogenetic trees, which were stored in the common nexus format, into newick format. In order to do this efficiently, I wrote the following one-liner. Change into a directory containing your nexus-formatted tree files, then enter in your bash shell: R […]

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BlastNg Away – Part 1

A post without spello in the title Today, I attempted to blast entire chloroplast genomes against NCBI’s nucleotide database via the BLASTn command-line tool. Since typical plastomes are between 150,000 and 160,000 bp in length, BLASTn searches that are conducted remotely take approximately 20 min. on average. time blastn -db nt -query myinputseq.fasta -remote -out […]

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