SEQ-EM specifications


Unique identifier OMICS_07409
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Registration required Yes
Maintained Yes


No version available


  • person_outline Bogdan Pasaniuc

Publication for SEQ-EM

SEQ-EM citations


Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis

PLoS One
PMCID: 3282730
PMID: 22363693
DOI: 10.1371/journal.pone.0031630

[…] uarantees the finding of all matches and reports a configurable maximum number of equally best matches. Perfect matches are given preference over matches containing mismatches.miRNAkey: The tool uses SEQ-EM algorithm to optimize the distribution of multiply-aligned-reads among the observed miRNAs, rather than discarding them. Reads counting is generated for each sample (i.e. sequencing lane), and […]


Performance comparison and evaluation of software tools for microRNA deep sequencing data analysis

Nucleic Acids Res
PMCID: 3378883
PMID: 22287634
DOI: 10.1093/nar/gks043

[…] equencing reads of the genome using MegaBLAST, while miRTRAP () uses the BLAST approach. SOAP2 is employed in mirTools, which can reduce computer memory usage and increase the alignment speed (). The SEQ-EM algorithm is applied by miRNAkey to optimize the distribution of multiple aligned reads among the observed miRNAs, before mapping using a reference database of known miRNAs with the Burrows–Whe […]

SEQ-EM institution(s)
Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA, USA; International Computer Science Institute, Berkeley, CA, USA; Molecular Microbiology and Biotechnology Department, Tel-Aviv University, Tel-Aviv, Israel; The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
SEQ-EM funding source(s)
Supported by National Science Foundation grant HS-071325412 and by the Israel Science Foundation grant no. 04514831.

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