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motif scan
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MOTIF Search allows you to search for motifs in protein sequences using various databases and profiles. You can enter a sequence ID, a local file name, or sequence data, and select motif libraries, cut-off scores, and user-defined profiles.
MEME Suite is a collection of tools for discovering and analyzing motifs in biological sequences. It includes tools for motif elicitation, enrichment, alignment, comparison, and target prediction.
ScanProsite tool allows you to scan proteins for matches against the PROSITE collection of motifs as well as against your own patterns. You can submit protein sequences, motifs or a combination of both and choose different options and output formats.
Protein motif scan Protein motifs are small regions of protein three-dimensional structure or amino acid sequence shared among different proteins. They are recognizable regions of protein structure that may (or may not) be defined by a unique chemical or biological function. 1. Protein sequence: Full Length: 0
MotifScan is a tool to detect and test the enrichment of known motifs in input genomic regions. It can also integrate epigenomic variation and transcription factor binding data to identify transcription activators.
Find and compare motifs in protein and DNA sequences using various databases and tools. Learn about motif databases, background information, and references for each tool.
Scansite features Scan a Protein by identifier* or input sequence Search Database using a Scansite motif, a user-defined motif, the quick matrix method, or multiple motifs Find protein sequence match using sequence patterns or regular expressions Scan orthologs Predict localization of proteins Calculate Molecular Weight and Isoelectric Point
The scanMotifGenomeWide.pl script will take a motif file (may contain multiple motifs) and look for instances across the genome. The basic command looks like this (output file is sent to stdout): scanMotifGenomeWide.pl [options] scanMotifGenomeWide.pl pu1.motif mm9 -bed > pu1.sites.mm9.bed The motif file and genome arguments are required. You man look for several motifs ...
Find presence of any known protein motif (Prosite and Pfam) in a protein sequence.
This function scans the promoter regions of protein-coding genes for transcription factor (TF) motifs. It extracts promoter sequences using an Ensembl database (EnsDb) and then searches these sequences for TF binding motifs using position frequency matrices (PFMs). The Seurat object is updated with a matrix of motif-gene matches, a list of target genes for each TF, and additional motif ...