SeqMap specifications

Information


Unique identifier OMICS_09522
Name SeqMap
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Stable
Maintained No

Documentation


Maintainer


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Publications for SeqMap

SeqMap in publications

 (47)
PMCID: 5841419
PMID: 29531832
DOI: 10.1038/s41420-018-0036-7

[…] in the hg-u133_plus_2.0 array to lncrnas, according to previous studies, , . first, we re-mapped the probes (probe sets) of affymetrix hg-u133_plus_2.0 array to the human genome (grch38) using seqmap. the probes (probe sets) were retained when they were uniquely mapped to the human genome with no mismatch. second, we matched the chromosomal position of the above probes (probe sets) […]

PMCID: 5671410
PMID: 29096247
DOI: 10.1016/j.tranon.2017.09.005

[…] batch effects when combining batches of gene expression dataset . lncrna expression of the nac-treated patients was obtained by remapping the probes of the array to human genome (grch38/hg38) using seqmap and then matching the probes to the lncrna chromosomal positions from gencode (release 24, grch38) , , . a total of 616 probes corresponding to 463 lncrnas were obtained in the end. lncrna […]

PMCID: 5549759
PMID: 28749988
DOI: 10.1371/journal.pgen.1006926

[…] in a rapid mode for 50-bp single-end runs (yielding 14–62 million reads per sample). reads corresponding to abundant noncoding rna sequences, such as rrnas and trnas, and mirnas were removed using seqmap [], and the remaining reads with a length of 24–33 nt were then mapped to the retrotransposon consensus sequences that were used for the mrna analysis by seqmap, allowing two mismatches. […]

PMCID: 5642505
PMID: 29050230
DOI: 10.18632/oncotarget.18751

[…] a mean of 0 and a standard deviation (sd) of 1. first, affymetrix hg-u133a probesets from the affymetrix website (http://www.affymetrix.com) were re-mapped to the human genome (grch38/hg38) using seqmap33 with no mismatch []. second, the chromosomal positions of those probes, which were uniquely mapped to the human genome, were matched to the chromosomal positions of lncrnas derived […]

PMCID: 5302127
PMID: 28114302
DOI: 10.1038/nature21025

[…] to 66 7mer seed families with identical sequence from nucleotides 2-8. 8mer binding sites for these seeds, defined as in, were identified in the 3' utrs of all expressed genes (fpkm > 0) using seqmap (v1.0.12). the locations were then transformed to genomic coordinates and extended 10 nt upstream and downstream to obtain a seed match region (excluding sites on exon-exon junctions). […]


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SeqMap institution(s)
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Biostatistics, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA; Section of Pediatric Hematology/Oncology, Riley Hospital for Children, Indianapolis, IN, USA

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