Open Source replacement for MatInspector (prediction transcription factor binding sites)

Does anyone know a replacement for MatInspector along with the appropriate database?

It should be open source.

Critical: If you know a tool that does the same, do you know if its performance is comparable?

transcription-factor

• 715 views • link

written 4.8 years ago by mschmid

0 answers

No answers yet.

More posts like this

Draw phylogenetic tree with zoom into a specific clade
written 9.4 years ago by mschmid

Does anyone know a nice tool where it is possible to draw a phylogenetic tree but where you have also the option to zoom into …
All vs. all pairwise sequence aligment
written 9.5 years ago by mschmid

I have a fasta file with amino acid sequences. Now I want to align every sequence with every other (so it's **pairwise**). The outcome should …
Tool for Converting STR Sequence Data to Bracketed Sequence
written 10.0 years ago by lattarulol •

Can anyone recommend a tool (preferably open source) that converts STR sequence data to its bracketed notation? For example, with a repeat motif of TCTA, …
Forum: How can I illustrate the importance of open source software in bioinformatics for people out…
written 10.2 years ago by Keith Callenberg

I think it's safe to say that the majority of people in science, technology, and engineering fields are now comfortable with the idea of open …
biopython: Bio.motifs : 'Motif' has no attribute 'parse'
written 10.4 years ago by John •

Hi, I am trying to parse MEME formatted motif using Bio.motifs object. >>> list(Motif.parse(open("test.meme"),"MEME")) ... AttributeError: type object 'Motif' has no attribute 'parse' Does anyone …
Programm/tool for drawing promoter motif image
written 10.5 years ago by teresa.noviello89 •

Hi. I have a list of putative TF binding site on the promoter of a studied gene. I have both the start-end and the sequence …
Database for Antibiotic/Antimicrobial products of Bacteria
written 10.7 years ago by mschmid

Does anyone know a good database to find Antimicrobial agents produced by Bacteria? I want to use it on a de novo assembled bacterial genome. …
Where to put start for assembled genome/plasmid
written 10.8 years ago by mschmid

If you have a closed bacterial genome or plasmid, what are the general rules where to put the start. With start I mean where the …
Nice open source alternative to "contig viewer" in SeqMan Pro
written 11.0 years ago by mschmid

Today I had a little assembly course. They showed us the closed source SW "SeqMan Pro". In this SW you have a nice mode, where …
Favorite Splice Site Prediction/Evaluation Tools
written 13.7 years ago by Alex Paciorkowski

Does anyone have a favorite splice site prediction / evaluation tool? (This would be for evaluating variants in the human genome). I am familiar with …