Molecular Biology Workshop - resources - Yunlong Liu Lab |
Resource
Nucleic Acids Research
http://nar.oxfordjournals.org/
by category: http://www.oxfordjournals.org/nar/database/c
DATABASE: The Journal of Biological Databases and Curation
http://database.oxfordjournals.org/
UCSC Genome Browser
Live Demo
Demo sequence:
ATGCACTTGAGCAGGGAAGAAATCCACAAGGACTCACCAGTCTCCTGGTC
TGCAGAGAAGACAGAATCAACATGAGCACAGCAGGAAAAGTAATCAAATG
CAAAGCAGCTGTGCTATGGGAGTTAAAGAAACCCTTTTCCATTGAGGAGG
TGGAGGTTGCACCTCCTAAGGCCCATGAAGTTCGTATTAAGATGGTGGCT
GTAGGAATCTGTGGCACAGATGACCACGTGGTTAGTGGTACCATGGTGAC
CCCACTTCCTGTGATTTTAGGCCATGAGGCAGCCGGCATCGTGGAGAGTG
TTGGAGAAGGGGTGACTACAGTCAAACCAGGTGATAAAGTCATCCCACTC
GCTATTCCTCAGTGTGGAAAATGCAGAATTTGTAAAAACCCGGAGAGCAA
CTACTGCTTGAAAAACGAGTAGGTTTCTGATGCTCTCCCTGCGCAGACAT
TGAGTTTGCAC
DNA – Restriction Enzyme
http://rna.lundberg.gu.se/cutter2/
DNA – Nucleotide sequence homology search
RNA – Sequence translation
http://ca.expasy.org/tools/dna.html
RNA – mRNA secondary structure prediction
RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi)
mFOLD (frontend.bioinfo.rpi.edu/applications/mfold/cgi-bin/rna-form1.cgi)
GeneBee (http://www.genebee.msu.su/services/rna2_reduced.html)
Gene regulation – Transcription factor binding sites
Match (http://www.gene-regulation.com/cgi-bin/pub/programs/match/bin/match.cgi)
TESS (http://www.cbil.upenn.edu/cgi-bin/tess/tess)
SignalScan (http://www-bimas.cit.nih.gov/molbio/signal/)
TFScan (http://mobyle.pasteur.fr/cgi-bin/portal.py?form=tfscan)
Gene regulation – microRNA binding sites
TargetScan (http://www.targetscan.org/)
Miranda (http://cbio.mskcc.org/mirnaviewer/)
PicTar (http://pictar.mdc-berlin.de/)
PITA (http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html)
miR2Disease (http://www.miR2Disease.org)
Gene regulation – Alternative splicing
FAST-DB (http://www.fast-db.com/)
UCSC genome browser (http://genome.ucsc.edu)
Wikipage:
https://compbio.iupui.edu/support/wiki/index.php/KB