BLAST and Molecular Modeling

Bioinformatics along with molecular modelling has become one of the main mind-blowing and growing area in biological science fields that anyone would do while having lowest facilities like just a computer and an internet connection.

Here these are some of few PDF files that you would follow and try to learn by your self.

Important Links

NCBI Databases

https://www.ncbi.nlm.nih.gov/search/

Expassy

https://www.expasy.org/

http://expasy.org/resources

NCBI BLAST

https://blast.ncbi.nlm.nih.gov/Blast.cgi

Nucleotide BLAST

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Protein BLAST

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Smart BLAST

https://blast.st-va.ncbi.nlm.nih.gov/blast/smartblast/

Conserved Domains

https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

Secondary structures of Proteins

http://www.biogem.org/tool/chou-fasman/index.php

Swiss Modeling

https://swissmodel.expasy.org/

Globular or not ?

http://globplot.embl.de/cgiDict.py

Transmembrane Protein ?
http://mendel.imp.ac.at/sat/DAS/DAS.html

RNA Secondary Structure Prediction

http://www.biogem.org/tool/nussinov/

Other structure related tools

http://www.biogem.org/tools.html

Protein Structure compare

https://www.rcsb.org/#Category-analyze

http://www.rcsb.org/pdb/workbench/workbench.do

Physiochemical Properties

https://web.expasy.org/protparam/

Protein Seq. to Nucletide Seq.

http://www.bioinformatics.org/sms2/rev_trans.html

Restriction enzymes

http://www.restrictionmapper.org/

https://www.genscript.com/tools/restriction-enzyme-map-analysis

https://www.genscript.com/tools.html?src=leftbar

Multiple sequence alignment program for three or more sequences

https://www.ebi.ac.uk/Tools/msa/clustalw2/

Contigs

http://doua.prabi.fr/software/cap3

NCBI Genome data viewer

https://www.ncbi.nlm.nih.gov/genome/gdv/browser/help/

All the files

  

R Software

Graphs

https://www.harding.edu/fmccown/r/

https://www.statmethods.net/graphs/creating.html

https://www.statmethods.net/graphs/creating.html

R for beginers

Enjoy !