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UCSC Archaea table browser
Get Microbial Data
BioMart Central server
GrameneMart Central server
Flymine server
EuPathDB server
EncodeDB at NHGRI
EpiGRAPH server
Send Data
Perform genome analysis and prediction with EpiGRAPH
ENCODE Tools
Gencode Partition an interval file
Random Intervals create a random set of intervals
Lift-Over
Convert genome coordinates between assemblies and genomes
Text Manipulation
Add column to an existing query
Compute an expression on every row
Concatenate queries tail-to-head
Condense consecutive characters
Convert delimiters to TAB
Merge Columns together
Create single interval as a new query
Cut columns from a table
Change Case of selected columns
Paste two files side by side
Remove beginning of a file
Select first lines from a Query
Select last lines from a Query
Trim leading or trailing characters
Convert Formats
BED-to-GFF converter
FASTA-to-Tabular converts FASTA file to tabular format
GFF-to-BED converter
Maf to BED Converts a MAF formated file to the BED format
MAF to Interval Converts a MAF formatted file to the Interval format
MAF to FASTA Converts a MAF formated file to FASTA format
Tabular-to-FASTA converts tabular file to FASTA format
FASTQ to FASTA converter
FASTA manipulation
Compute sequence length
Filter sequences by length
Concatenate FASTA alignment by species
FASTA-to-Tabular converts FASTA file to tabular format
Tabular-to-FASTA converts tabular file to FASTA format
FASTA Width formatter
RNA/DNA converter
Collapse sequences
Filter and Sort
Filter data on any column using simple expressions
Sort data in ascending or descending order
Select lines that match an expression
Join, Subtract and Group
Join two Queries side by side on a specified field
Compare two Queries to find common or distinct rows
Subtract Whole Query from another query
Group data by a column and perform aggregate operation on other columns.
Extract Features
Fetch Sequences
Extract Genomic DNA using coordinates from assembled/unassembled genomes
Fetch Alignments
Extract Pairwise MAF blocks given a set of genomic intervals
Extract MAF blocks given a set of genomic intervals
Stitch MAF blocks given a set of genomic intervals
Stitch Gene blocks given a set of coding exon intervals
MAF Coverage Stats Alignment coverage information
Join MAF blocks by Species
Filter MAF blocks by Species
Filter MAF blocks by Size
Extract MAF by block number given a set of block numbers and a MAF file
Filter MAF by specified attributes
Reverse Complement a MAF file
Get Genomic Scores
Wiggle-to-Interval converter
Aggregate datapoints such as phastCons, GERP, binCons, and others for a set of genomic intervals
Compute phastOdds score for each interval
Operate on Genomic Intervals
Intersect the intervals of two queries
Subtract the intervals of two queries
Merge the overlapping intervals of a query
Concatenate two queries into one query
Base Coverage of all intervals
Coverage of a set of intervals on second set of intervals
Complement intervals of a query
Cluster the intervals of a query
Join the intervals of two queries side-by-side
Get flanks returns flanking region/s for every gene
Fetch closest feature for every interval
Profile Annotations for a set of genomic intervals
Statistics
Summary Statistics for any numerical column
Count occurrences of each record
Correlation for numeric columns
Graph/Display Data
Histogram of a numeric column
Scatterplot of two numeric columns
Plotting tool for multiple series and graph types
GMAJ Multiple Alignment Viewer
Build custom track for UCSC genome browser
Regional Variation
Make windows
Feature coverage
Filter nucleotides based on quality scores
Mask CpG/non-CpG sites from MAF file
Fetch Indels from pairwise alignments
Fetch Indels from 3-way alignments
Estimate Indel Rates for 3-way alignments
Fetch substitutions from pairwise alignments
Estimate substitution rates for non-coding regions
Extract Orthologous Microsatellites from pair-wise alignments
Estimate microsatellite mutability by specified attributes
Multiple regression
Evolution
Branch Lengths Estimation
Neighbor Joining Tree Builder
dN/dS Ratio Estimation
Mutate Codons with SNPs
Metagenomic analyses
EMBOSS
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.
backtranseq Back translate a protein sequence
banana Bending and curvature plot in B-DNA
biosed Replace or delete sequence sections
btwisted Calculates the twisting in a B-DNA sequence
cai custom CAI codon adaptation index using custom codon usage file
cai CAI codon adaptation index
chaos Create a chaos game representation plot for a sequence
charge Protein charge plot
checktrans Reports STOP codons and ORF statistics of a protein
chips Codon usage statistics
cirdna Draws circular maps of DNA constructs
codcmp Codon usage table comparison
coderet Extract CDS, mRNA and translations from feature tables
compseq Count composition of dimer/trimer/etc words in a sequence
cpgplot Plot CpG rich areas
cpgreport Reports all CpG rich regions
cusp Create a codon usage table
cutseq Removes a specified section from a sequence
dan Calculates DNA RNA/DNA melting temperature
degapseq Removes gap characters from sequences
descseq Alter the name or description of a sequence
diffseq Find differences between nearly identical sequences
digest Protein proteolytic enzyme or reagent cleavage digest
dotmatcher Displays a thresholded dotplot of two sequences
dotpath Non-overlapping wordmatch dotplot of two sequences
dottup Displays a wordmatch dotplot of two sequences
dreg Regular expression search of a nucleotide sequence
einverted Finds DNA inverted repeats
epestfind Finds PEST motifs as potential proteolytic cleavage sites
equicktandem Finds tandem repeats
est2genome Align EST and genomic DNA sequences
etandem Looks for tandem repeats in a nucleotide sequence
extractfeat Extract features from a sequence
extractseq Extract regions from a sequence
freak Residue/base frequency table or plot
fuzznuc Nucleic acid pattern search
fuzzpro Protein pattern search
fuzztran Protein pattern search after translation
garnier Predicts protein secondary structure
geecee Calculates fractional GC content of nucleic acid sequences
getorf Finds and extracts open reading frames (ORFs)
helixturnhelix Report nucleic acid binding motifs
hmoment Hydrophobic moment calculation
iep Calculates the isoelectric point of a protein
infoseq Displays some simple information about sequences
isochore Plots isochores in large DNA sequences
lindna Draws linear maps of DNA constructs
marscan Finds MAR/SAR sites in nucleic sequences
maskfeat Mask off features of a sequence
maskseq Mask off regions of a sequence
matcher Finds the best local alignments between two sequences
megamerger Merge two large overlapping nucleic acid sequences
merger Merge two overlapping nucleic acid sequences
msbar Mutate sequence beyond all recognition
needle Needleman-Wunsch global alignment
newcpgreport Report CpG rich areas
newcpgseek Reports CpG rich region
newseq Type in a short new sequence
noreturn Removes carriage return from ASCII files
notseq Exclude a set of sequences and write out the remaining ones
nthseq Writes one sequence from a multiple set of sequences
octanol Displays protein hydropathy
oddcomp Find protein sequence regions with a biased composition
palindrome Looks for inverted repeats in a nucleotide sequence
pasteseq Insert one sequence into another
patmatdb Search a protein sequence with a motif
pepcoil Predicts coiled coil regions
pepinfo Plots simple amino acid properties in parallel
pepnet Displays proteins as a helical net
pepstats Protein statistics
pepwheel Shows protein sequences as helices
pepwindow Displays protein hydropathy
pepwindowall Displays protein hydropathy of a set of sequences
plotcon Plot quality of conservation of a sequence alignment
plotorf Plot potential open reading frames
polydot Displays all-against-all dotplots of a set of sequences
preg Regular expression search of a protein sequence
prettyplot Displays aligned sequences, with colouring and boxing
prettyseq Output sequence with translated ranges
primersearch Searches DNA sequences for matches with primer pairs
revseq Reverse and complement a sequence
seqmatchall All-against-all comparison of a set of sequences
seqret Reads and writes sequences
showfeat Show features of a sequence
shuffleseq Shuffles a set of sequences maintaining composition
sigcleave Reports protein signal cleavage sites
sirna Finds siRNA duplexes in mRNA
sixpack Display a DNA sequence with 6-frame translation and ORFs
skipseq Reads and writes sequences, skipping first few
splitter Split a sequence into (overlapping) smaller sequences
supermatcher Match large sequences against one or more other sequences
syco Synonymous codon usage Gribskov statistic plot
tcode Fickett TESTCODE statistic to identify protein-coding DNA
textsearch Search sequence documentation. Slow, use SRS and Entrez!
tmap Displays membrane spanning regions
tranalign Align nucleic coding regions given the aligned proteins
transeq Translate nucleic acid sequences
trimest Trim poly-A tails off EST sequences
trimseq Trim ambiguous bits off the ends of sequences
twofeat Finds neighbouring pairs of features in sequences
union Reads sequence fragments and builds one sequence
vectorstrip Strips out DNA between a pair of vector sequences
water Smith-Waterman local alignment
wobble Wobble base plot
wordcount Counts words of a specified size in a DNA sequence
wordmatch Finds all exact matches of a given size between 2 sequences
NGS Toolbox Beta
NGS: QC and manipulation
NGS: Mapping
Map with Bowtie
Map with BWA
Megablast compare short reads against nt and wgs databases
Parse blast XML output
NGS: SAM Tools
Filter SAM on bitwise flag values
Convert SAM to interval
SAM-to-BAM converts SAM format to BAM format
Merge BAM Files merges BAM files together
Generate pileup from BAM dataset
Filter pileup on coverage and SNPs
Pileup-to-Interval condenses pileup format into ranges of bases