Non-alphanumeric characters (from '-') are stripped.
All search keyword are used in searching links: e.g. bioinformatics links directory will search for links that contain all three keywords in title, description, or tags.
You can search for an exact phrase by enclosing the query in quotes: e.g. "bioinformatics links directory"
e.g. Search query "genomic sequences" dna will search for links containing the phrase "genomic sequences" and dna.
You can include OR uppercase keyword: e.g. dna OR rna looks for keywords dna or rna.
You can include - prefix or NOT uppercase keyword to define keywords that should not be included: e.g. dna OR rna NOT protein (alternatively: dna OR rna -protein) will look for links with keywords DNA or RNA, but not protein
The links from this subcategory have been moved. They are now located in Top : Sequence Comparison.
@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.
AlignMe (for Alignment of Membrane Proteins) can be used to examine detailed similarity between homologous proteins even if there is no notable sequence similarity. The predefined gap/weight sets have been optimized for membrane proteins, and so should be particularly useful for these difficult cases.
Alignment Annotator is a web service which annotates and renders sequence alignments using annotation services and the PDB. The annotated and colorized alignment can be downloaded as an interactive HTML file for web browsers.
This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.
COMA is a distant homology detection method based on sequence profile–profile comparison. COMA takes a protein sequence or multiple sequence alignment as input and searches for remote homologs in SCOP, PDB and PFAM databases.
HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.
HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.
InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for any species present in the Integr8 database (more than 1500 organisms). The method combines known interactions and clusters of orthologous proteins. The tool can be downloaded or used through the web application.
MaxAlign is a web server for maximizing usable data in an alignment. It maximizes the number of nucleotide (or amino acid) symbols present in gap-free columns by selecting the optimal subset of sequences to exclude from the alignment.
PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.
PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.