Epidemiology Laboratory
IRYCIS-Ramón y Cajal Hospital
EpiMolBio features summary
VIRUS
HIV
Calculates the percentage of acquired and transmitted DRM, relative to a reference sequence, from AA sequences of HIV Pol proteins and Capsid.
Detects any mutation (not only DRM) in HIV-1 or HIV-2 from sequences of Pol proteins, and their percentage relative to the reference sequence.
Generates a table displaying the most prevalent AA and its corresponding percentage at each position within the selected Pol protein sequence, facilitating the identification of the protein’s most conserved residue for each position.
SARS-CoV-2
Provides sequences in .fasta format of the chosen proteins from SARS-CoV-2, based on complete genomes, in NT or AA.
VARIABILITY
Markers allows the detection of mutations exclusive to each file compared to the rest of the input files.
Multiple Mutations enables the detection of mutation combinations providing their frequency of occurrence.
Codon function detects the codons that are different from those in the reference sequence and their frequency of occurrence.
Mutations by Position allows the detection of residues at one position or several combined positions providing their frequency of occurrence.
Determines the level of conservation of sequences of interest by reporting the most prevalent residue and its corresponding percentage. Additionally, it generates consensus sequences
Codon function presents the most conserved codon from an analyzed nucleotide sequence.
Provides consensus sequences and consensus of consensuses by performing multiple rounds of analysis.
Provides the Wu-Kabat variability coefficient of protein sequences to study the susceptibility of an amino acid position to evolutionary replacements.
Generates a set of parameters related to the frequency of mutations in a group of sequences, such as mutation frequency, conservation percentage, and average mutations per sequence. Uses BioJava 5.
homology
Searchs for a user-introduced target sequence among the sequences in the input file, obtaining the proportion of sequences per file that contain the target sequence.
Compares a user-introduced sequence with the input sequences to search for similar regions between them, defining the percentage of similarity between the sequences. Uses BioJava 5.
Extracts conserved sequence fragments from a set of input sequences. Allows searching within a specific region, choosing the fragment length, and establishing the conservation percentage.
TRACKER
Searchs for target sequences of interest within a set of longer sequences based on a reference sequence.
Searchs for proteins within a set of complete genomic sequences using the flanking sequences of the target protein.
ALIGNMENTS
Aligns AA and NT sequences using the MUSCLE v3.8.31 program.
Generates a graphic where sequences are compared by plotting points on a two-dimensional matrix, with each axis representing a sequence.
Automatically removes insertions from a sequence with respect to a reference with gaps after performing the alignment.
TOOLS
File Editing
Combines multiple .fasta files into a single .fasta file.
Removes duplicated sequences from one or multiple input .fasta files.
Filters sequences from .fasta files that contain one or multiple mutations chosen by the user.
Replaces a series of characters with others in both the header and the genetic sequence of one or multiple .fasta files.
Filters
Filters one or multiple “.fasta” format files using parameters from their headers.
Filters sequences from .fasta format files that have a specific set of characters in their headers.
Filters sequences from .fasta format files based on their quality, depending on the quantity of “?” (sequences in AA) or “N” (sequences in NT) they contain.
Other tools
Translates .fasta sequences from NT to AA.
Counts the total number of sequences in one or multiple .fasta files, or how many of those sequences contain mutations.
Automates the program’s functions by chaining them together to be executed sequentially without manual intervention.
VIRUS
HIV
Calculates the percentage of acquired and transmitted DRM, relative to a reference sequence, from AA sequences of HIV Pol proteins and Capsid.
Detects any mutation (not only DRM) in HIV-1 or HIV-2 from sequences of Pol proteins, and their percentage relative to the reference sequence.
Generates a table displaying the most prevalent AA and its corresponding percentage at each position within the selected Pol protein sequence, facilitating the identification of the protein’s most conserved residue for each position.
SARS-CoV-2
Provides sequences in .fasta format of the chosen proteins from SARS-CoV-2, based on complete genomes, in NT or AA.
VARIABILITY
Markers allows the detection of mutations exclusive to each file compared to the rest of the input files.
Multiple Mutations enables the detection of mutation combinations providing their frequency of occurrence.
Codon function detects the codons that are different from those in the reference sequence and their frequency of occurrence.
Mutations by Position allows the detection of residues at one position or several combined positions providing their frequency of occurrence.
Determines the level of conservation of sequences of interest by reporting the most prevalent residue and its corresponding percentage. Additionally, it generates consensus sequences
Codon function presents the most conserved codon from an analyzed nucleotide sequence.
Provides consensus sequences and consensus of consensuses by performing multiple rounds of analysis.
Provides the Wu-Kabat variability coefficient of protein sequences to study the susceptibility of an amino acid position to evolutionary replacements.
Generates a set of parameters related to the frequency of mutations in a group of sequences, such as mutation frequency, conservation percentage, and average mutations per sequence.
homology
Searchs for a user-introduced target sequence among the sequences in the input file, obtaining the proportion of sequences per file that contain the target sequence.
Compares a user-introduced sequence with the input sequences to search for similar regions between them, defining the percentage of similarity between the sequences.
Extracts conserved sequence fragments from a set of input sequences. Allows searching within a specific region, choosing the fragment length, and establishing the conservation percentage.
TRACKER
Searchs for target sequences of interest within a set of longer sequences based on a reference sequence.
Searchs for proteins within a set of complete genomic sequences using the flanking sequences of the target protein.
ALIGNMENTS
Aligns AA and NT sequences using the MUSCLE v3.8.31 program.
Generates a graphic where sequences are compared by plotting points on a two-dimensional matrix, with each axis representing a sequence.
Automatically removes insertions from a sequence with respect to a reference with gaps after performing the alignment.
TOOLS
File Editing
Combines multiple .fasta files into a single .fasta file.
Removes duplicated sequences from one or multiple input .fasta files.
Filters sequences from .fasta files that contain one or multiple mutations chosen by the user.
Replaces a series of characters with others in both the header and the genetic sequence of one or multiple .fasta files.
Filters
Filters one or multiple “.fasta” format files using parameters from their headers.
Filters sequences from .fasta format files that have a specific set of characters in their headers.
Filters sequences from .fasta format files based on their quality, depending on the quantity of “?” (sequences in AA) or “N” (sequences in NT) they contain.
Other tools
Translates .fasta sequences from NT to AA.
Counts the total number of sequences in one or multiple .fasta files, or how many of those sequences contain mutations.
Automates the program’s functions by chaining them together to be executed sequentially without manual intervention.