Useful links

Useful links

 

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

[link]http://www.ebi.ac.uk/Tools/emboss/align/index.html for pairwise alignment
 

Protein analysis

[link]http://www.expasy.org/tools/dna.html Translation of DNA into protein sequences

[link]http://elm.eu.org/ 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]https://blast.ncbi.nlm.nih.gov/Blast.cgi for Blast searches
[link]Reverse complementation

[link]https://www.arabidopsis.org/portals/genAnnotation/genome_annotation_tools/cis_element.jsp 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]http://www.arabidopsis.org
[link]http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi
[link]http://phytozome.net

[link]http://wheat.pw.usda.gov/GG2/index.shtml GrainGenes - wheat and oat

[link]http://cggc.agtec.uga.edu/index.asp Comparative Grass Genomics Centre

[link]http://www.gramene.org/ Comparative Grass Genomics Gramene

[link]http://www.maizegdb.org/ Maize

[link]http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp Rice

[link]http://www.tigr.org/tdb/e2k1/osa1/index.shtml Rice

[link]http://rgp.dna.affrc.go.jp/IRGSP/index.html Rice[link]

Primer design
[link]http://primer3.ut.ee/ can exclude sequence parts and regards desired PCR product size
[link]http://signal.salk.edu/tdnaprimers.2.html for T-DNA primer design

[link]artificial miRNA design for efficient gene knockdown

Cas9 / gRNA design

www.e-crisp.org/E-CRISP/

 

Databases for expression analysis (microarrays) in Arabidopsis thaliana
genevestigator.com/gv/
[link]http://www.plexdb.org

 

Literature mining

[link]https://apps.webofknowledge.com/  Literature search

[link]PubMed  Literature search

 

Literature management

www.mendeley.com

www.docear.org

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