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Showing 17 records out of 17 total

Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Four tools for multiple alignments.
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website, CLI, GUI - tool
Multiple alignment of nucleic acid and protein sequences.
Categories: proteomics, (protein sequences and identification, similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Redundancy reduction in a set of aligned or unaligned sequences
Categories: proteomics, (families, patterns and profiles, similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Positional dependent information contents of aligned RNA/DNA or amino acid sequences are useful for the display of consensus sequences and for finding optimal search windows used in sequence analysis. The program calculates the positional information content of mono or poly nucleotides/amino acids from a FASTA file of aligned sequences and writes a Postscript (or encapsulated Postscript, EPS) file that can be viewed and included in text processors
Categories: proteomics, (protein sequences and identification, similarity search/alignment), genomics, (sequence alignment, similarity search) - Software type(s): website, CLI - tool
LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally.
Categories: similarity search/alignment, sequence alignment - Software type(s): website - tool
The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. MaxAlign maximizes the number of characters that are present in gap-free columns. It can be used prior to any phylogenetic analysis as well as in other situations where this form of alignment clean up is useful, such as the presence of badly aligned or truncated sequences.
keywords: alignment analysis
Categories: genomics, (sequence alignment, similarity search), systems biology - Software type(s): website, CLI, GUI - tool
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
Categories: proteomics, (families, patterns and profiles, similarity search/alignment) - Software type(s): website - tool
Protein sequence logos using relative entropy.
Categories: proteomics, (families, patterns and profiles, similarity search/alignment) - Software type(s): website - tool
Protein sequence alignment viewed as sequence logos. The total height of the sequence information part is computed as the relative entropy between the observed fractions of a given symbol and the respective a priori probabilities.
Categories: similarity search/alignment - Software type(s): website - tool
This server calculates the protein sequence variability within a multiple sequence alignment using several variability metrics. Subsequently, the server can perform several tasks, such as masking the variability in the reference sequence, returning conserved fragments or mapping the sequence variability onto a provided 3D-structure.
keywords: alignment analysis
Categories: proteomics, (families, patterns and profiles, similarity search/alignment) - Software type(s): website - tool
Seq2Logo is a web-based sequence logo method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.
Categories: proteomics, (families, patterns and profiles, similarity search/alignment) - Software type(s): website - tool
SeqLogos generates sequences logos from amino acid sequence alignment. Sequences logos are useful tools to visualize sequence patterns and represent a more informative alternative to consensus sequence
Categories: similarity search/alignment - Software type(s): website - tool
This server calculates the variability in each column of a multiple sequence alignment using the Shannon entropy (H) function.
keywords: alignment analysis
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website, CLI - tool
A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures. Includes M-Coffee, R-Coffee, Expresso, PSI-Coffee, iRMSD-APDB.
Categories: similarity search/alignment, sequence alignment - Software type(s): website - tool
T-Coffee is a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods.
Categories: similarity search/alignment, sequence alignment - Software type(s): website - tool
T-Coffee is a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods.
Categories: proteomics, (families, patterns and profiles, similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position.