GenomeTools
Posted: 2014-09-17 Filed under: academic, drawing, slackbuilds | Tags: gene, genome, genometools, graphics, gt, inkscape, ugene, unipro Leave a commentI need to export gene coordinates and exon organisation as a figure. I have prepared the annotations in UniPro Ugene, which I have installed from SBo. A nice tool for graphical representation of such data is provided by the GenomeTools software. It can be easily installed from SBo, too. Read the rest of this entry »
Amino acid sequence as a column
Posted: 2014-08-19 Filed under: academic | Tags: amino acid, embassy, emboss, protein, sequence Leave a commentI need to present an amino acid sequence as a column, so I can paste it in a spreadsheet document (to serve as a reference to other analyses). There is a relatively straightforward way to do this. Read the rest of this entry »
Zotero bibliography manager
Posted: 2014-05-30 Filed under: academic, office, slackbuilds | Tags: bibliography, references, slackbuilds, zotero 2 CommentsI have been looking for a good bibliography manager for Linux. I have used Bibus in the past, it it does not seem to work with the new versions of OpenOffice.org or LibreOffice. Luckily, I got a great tip from Ryan P.C. McQuen — Zotero. Read the rest of this entry »
Cell values as rows in a spreadsheet
Posted: 2014-04-17 Filed under: academic | Tags: Cell values, gnumeric, sort, spreadsheet Leave a commentI have some spreadsheet data where the first column lists the position of a certain amino acid within a protein. There are many amino acid sites that are skipped, therefore the rows do not follow the actual, uninterrupted, amino acid sequence. Read the rest of this entry »
Custom protein topology schemes
Posted: 2014-04-14 Filed under: academic | Tags: DOG, DomainDraw, ELM, JSON, lang, MyDomains, NetNGlyc, NetPhos, PFAM, PROTTER, SMART 1 CommentI need to generate custom graphics of several proteins (in fact nearly 30). I have the domain organisation predicted at the SMART database, the N-glycosylation sites at NetNGlyc and the possible phosphorylation targets at NetPhos. I also have identified short functional motifs at ELM.
Now I need a program that can generate custom graphics that would combine all of these neatly. Read the rest of this entry »
Slackalaxy 