Useful links

Useful links


Sequence alignment 
[link]T-coffee for alignment of multiple sequences
[link]ClustalW for classical alignments of multiple sequences

[link] for pairwise alignment

Protein analysis

[link] Translation of DNA into protein sequences

[link] finds functional sites in proteins

[link]IntAct Protein interaction database

[link]String Protein interaction database

[link]N-Browse Protein interaction database

[link]SignalP5 Signal-Peptide prediction program

[link]EffectorP Fungal effector prediction program


Sequence analysis, comparison and manipulation
[link] for Blast searches
[link]Reverse complementation

[link] for promoter analysis

[link]AtcisDB Arabidopsis cis-regulatory element database

[link]Motif Finder Motif Analysis in Promoter or Upstream Gene Sequences 


Databases for genomic sequences of various plants [link]

[link] GrainGenes - wheat and oat

[link] Comparative Grass Genomics Centre

[link] Comparative Grass Genomics Gramene

[link] Maize

[link] Rice

[link] Rice

[link] Rice[link]

Primer design
[link] can exclude sequence parts and regards desired PCR product size
[link] for T-DNA primer design

[link]artificial miRNA design for efficient gene knockdown

Cas9 / gRNA design


Databases for expression analysis (microarrays) in Arabidopsis thaliana


Literature mining

[link]  Literature search

[link]PubMed  Literature search


Literature management

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