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Protocols

SEQ-EM specifications

Information


Unique identifier OMICS_07409
Name SEQ-EM
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

Versioning


No version available

Maintainer


  • person_outline Bogdan Pasaniuc <>

Publication for SEQ-EM

SEQ-EM citations

 (6)
library_books

Evaluation of Bioinformatics Approaches for Next Generation Sequencing Analysis of microRNAs with a Toxicogenomics Study Design

2018
PMCID: 5808213
PMID: 29467792
DOI: 10.3389/fgene.2018.00022

[…] multiple mirnas are handled differently by all four tools. in this step, tools distribute mapped reads to known mirnas in their own way and output the expression values accordingly. mirnakey employs seq-em for additional preferences for the allocation of multiply aligned reads. in this step, we had both the multiple mapping and single mapping values for srnabench and mirdeep2 which were computed […]

library_books

Acquisition of an oncogenic fusion protein is sufficient to globally alter the landscape of miRNA expression to inhibit myogenic differentiation

2017
PMCID: 5675615
PMID: 29152063
DOI: 10.18632/oncotarget.19693

[…] and amplification of the samples. mirnakey, was used for data analysis at default settings. the pipeline clips the illumina 3′ adaptor sequences, maps the clipped reads to mirbase and uses the seq-em algorithm to estimate the distribution of multiply mapped reads across the observed mirnas. sequences less than 16 bases after adaptor clipping were removed. the read counts obtained […]

library_books

Acquisition of an oncogenic fusion protein serves as an initial driving mutation by inducing aneuploidy and overriding proliferative defects

2016
PMCID: 5325330
PMID: 27588498
DOI: 10.18632/oncotarget.11716

[…] from deep sequencing experiments, was used for data analysis at default settings. the pipeline clips the illumina 3′ adaptor sequences from the reads, maps the clipped reads to mirbase and uses the seq-em algorithm to estimate the distribution of multiply mapped reads across the observed mirnas. sequences less than 16 bases after adaptor clipping were removed. the read counts obtained […]

call_split

Comparative transcriptomic analysis reveals the oncogenic fusion protein PAX3 FOXO1 globally alters mRNA and miRNA to enhance myoblast invasion

2016
PMCID: 4972903
PMID: 27454080
DOI: 10.1038/oncsis.2016.53
call_split See protocol

[…] of the samples. mirnakey was used for data analysis at default settings. the pipeline clips the illumina 3' adapter sequences from the reads, maps the clipped reads to mirbase and uses the seq-em algorithm to estimate the distribution of multiply mapped reads across the observed mirnas. sequences <16 bases after adaptor clipping were removed. the read counts obtained were then used […]

library_books

Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model

2013
PMCID: 3585423
PMID: 23459507
DOI: 10.3389/fgene.2013.00020

[…] mouse genome (mm9) and mirbase_v18 (mmu sequences) and further processed using mirdeep2.pl scripts. the csv files for mirna expression from mirdeep2 were used for further analysis., incorporates the seq-em algorithm to optimize the distribution of multiple aligned reads among the mirnas expressed, and does not discard them. output is read counts and rpm index (the read count normalized […]

library_books

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis

2012
PMCID: 3282730
PMID: 22363693
DOI: 10.1371/journal.pone.0031630

[…] 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), […]


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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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