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EGassembler

Aligns and merges sequence fragments resulting from shotgun sequencing or gene transcripts (EST) fragments in order to reconstruct the original segment or gene
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Sequence Cleaning Repeat Masking Vector Masking Organelle Masking Sequence Assembly


PROJECT NAME EMAIL ADDRESS

Query sequences

TEXT DATA , Please paste your sequences (FASTA format)
FILE UPLOAD(FASTA format)

Options

number of CPUs
SPEED
Normal
Quick ; 5-10% less sensitive, 2-5 times faster than default
Rush ; about 10% less sensitive, 4->10 times faster than default
Slow ; 0-5% more sensitive, 2-3 times slower than default
Does not mask low_complexity DNA or simple repeats
Only masks low complex/simple repeats (no interspersed repeats)
Does not mask small RNA (pseudo) genes
Sets cutoff score for masking repeats when using -lib
Repeats Library
Human
Using your custom repeats library
Using EGrep repeats library (Our custom repeats library)
Using RepBase repeats library
Using TREP repeats library
Using TIGR repeats library
Writes alignments in .align output file
Returns repetitive regions masked with Xs rather than Ns
Reports simple repeats that may be polymorphic (in .poly output file)
Creates an additional output file in ACeDB format
Creates an additional output file in cross_match format (for parsing)
Home KEGG GenomeNet Kanehisa Laboratory

Reference:
Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, Itoh M, Kanehisa M, Endo T, Goto S (2006)
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res. 34:W459-462.