Useful links and documents Sequence alignment T-coffee for alignment of multiple sequences ClustalW for classical alignments of multiple sequences for pairwise alignment Multiple sequence alignment with amino acid substitution consistency Protein analysis Translation of DNA into protein sequences finds functional sites in proteins Protein interaction database String Protein interaction database N-Browse Protein interaction database SignalP5 Signal-Peptide prediction program EffectorP Fungal effector prediction program Detection of repeats in protein sequence Tool for the prediction of SUMOylation sites and SUMO-interaction motifs in protein of interest http://sumosp.biocuckoo.org/ Sequence analysis, comparison and manipulation https://blast.ncbi.nlm.nih.gov/Blast.cgi for Blast searches https://solgenomics.net/tools/blast/ for Blast searches Reverse complementation https://www.arabidopsis.org/portals/genAnnotation/genome_annotation_tools/cis_element.jsp for promoter analysis AtcisDB Arabidopsis cis-regulatory element database Motif Finder Motif Analysis in Promoter or Upstream Gene Sequences Plasmid annotation tool Databases for genomic sequences of various plants http://www.arabidopsis.org http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi http://phytozome.net GrainGenes - wheat and oat Comparative Grass Genomics Centre Comparative Grass Genomics Gramene Maize Solanacea (Tomato, Tobacco etc.) Rice Rice 2 Rice 3 Primer design can exclude sequence parts and regards desired PCR product size for T-DNA primer design artificial miRNA design for efficient gene knockdown https://vigs.solgenomics.net/ for VIGS construct design Cas9 / gRNA design www.e-crisp.org/E-CRISP/ Databases for expression analysis (microarrays) in Arabidopsis thaliana https://genevestigator.com/gv/ http://www.plexdb.org Literature mining https://apps.webofknowledge.com/ Literature search PubMed Literature search Literature management www.mendeley.com www.docear.org Bioinformatische Werkzeugsammlung https://www.mpimp-golm-mpg.de/719693/Bioinformatik-Tools