:: DESCRIPTION
LogOddsLogo is a web based application designed to make the generation of sequence logos from biological sequence alignments simple.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation:
Log-Odds Sequence Logos.
Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF.
Bioinformatics. 2014 Oct 6. pii: btu634
:: DESCRIPTION
The CorreLogo generates for a given RNA or DNA sequence alignment a three-dimensional representation in VRML format and JavaView JVX format. The generated model contains quantities like mutual information, composition and single column information (“conservation”) in one three-dimensional representation. This can be useful for visual inspection of the properties of a nucleotide sequence alignment and for RNA secondary structure prediction.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
E. Bindewald, T.D. Schneider, B.A. Shapiro:
CorreLogo: An online server for 3D sequence logos of RNA and DNA alignments
Nucleic Acids Res. 2006 Jul 1;34 (Web Server issue):W405-11.
:: DESCRIPTION
Program enoLOGOS generates LOGOs of transcription factor DNA binding sites from various types of input matrices. It can utilize standard count matrices, probability matrices or matrices of “energy” values (i.e., log-frequencies).
::DEVELOPER
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W389-92.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
:: DESCRIPTION
Logo2PWM is a tool to convert sequence logo to position weight matrix
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
No
:: MORE INFORMATION
Citation
Logo2PWM: a tool to convert sequence logo to position weight matrix.
Gao Z, Liu L, Ruan J.
BMC Genomics. 2017 Oct 3;18(Suppl 6):709. doi: 10.1186/s12864-017-4023-9.
:: DESCRIPTION
WebLogo is a web based application designed to make the generation of sequence logos easy and painless. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Crooks GE, Hon G, Chandonia JM, Brenner SE
WebLogo: A sequence logo generator,
Genome Research, 14:1188-1190, (2004)
:: DESCRIPTION
LOLA (LOgos Look Amazing) is a tool for generating sequence logos using Position Weight Matrix based protein profiles. LOLA allows you to generate custom sequence logos by setting parameters such as logo height, trim percentage, and residue colour scheme. You can also generate “logo trees” based on clustered protein profiles to analyze binding motif classes. Sequence logos and logo trees can be saved in various formats including PDF, PNG, and JPEG.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Tonikian, R. et al.(2008)
A Specificity Map for the PDZ Domain Family.
PLOS Biology, 6, 9: 2043-2059.