SeqMap statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.


Citations per year

Citations chart

Popular tool citations

chevron_left Read alignment chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases


To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.


SeqMap specifications


Unique identifier OMICS_00684
Name SeqMap
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format FASTA, raw DNA sequence format
Output format Eland
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 1.0.13
Stability Stable
Source code URL
Maintained Yes


Add your version



  • person_outline Hui Jiang <>
  • person_outline Wing Hung Wong <>

Publication for SeqMap

SeqMap in pipelines

PMCID: 4869193
PMID: 27183847
DOI: 10.1186/s12864-016-2697-z

[…] from repeatmasker ( remaining trnas, rrnas and simple repeats were excluded. all other ncrnas like long terminal repeats (ltrs) were retained. for read mapping the seqmap tool, which is designed to map short sequences to the genome, was used with the argument ‘output all matches’ with no mismatches allowed []., so far, no pirna reference dataset for medaka […]

PMCID: 3603004
PMID: 23264558
DOI: 10.1093/mp/sss160

[…] screening, we followed the procedure described by ; briefly, a maximum of three mismatches was allowed and up to 2 nt overhanging nucleotides at the 5’ and/or 3’ end. alignments were performed using seqmap (). the sum of abundances of all the variants identified per each mirna candidate was reported for each small rna library (see supplemental figure 2)., all mirnas and sirna-like mirna loci […]

PMCID: 3252374
PMID: 22085832
DOI: 10.1186/1471-2164-12-560

[…] used in the constructions.), searches of human genome hg18 downloaded from ucsc genome browser ( were conducted using all of the sequences that hnf4α bound in pbm3 using seqmap []. alu and non alu repeats with hnf4α sites were identified by comparing the hnf4α genome-wide search results to the repeat coordinates obtained from repeat masker track version 3.2.7 in ucsc […]

PMCID: 3333190
PMID: 22369359
DOI: 10.1186/1471-2164-12-S3-S7

[…] data. the spliced leaders (sls) in the trans-spliced sequences were replaced with splice acceptor sequence “ag” for the subsequent mapping. the sequences were aligned to the kh assembly [] using seqmap [] for the 36-cycle reads, or to blat [] for the 48-cycle reads, because of the high rate of cis-splicing. because of the highly polymorphic genic features of this organism [], we used a 90% […]

To access a full list of citations, you will need to upgrade to our premium service.

SeqMap in publications

PMCID: 5816619
PMID: 29453409
DOI: 10.1038/s41598-018-21581-w

[…] actualized by r package ‘affy’. lncrna profile mining was mainly referenced to method proposed by du et al.. briefly, we mapped the probe sets ids from affymetrix hg-u133a to human genome, and seqmap was used to avoid mismatching. then, the chromosomal positions according these probe ids were used to identify corresponding positions of lncrna. finally, 569 annotated lncrna transcripts […]

PMCID: 5552786
PMID: 28798320
DOI: 10.1038/s41598-017-07114-x

[…] tags of 16–19 bp using in-house developed perl scripts. reverse complements of tags ending with ‘catg’ were also considered in the final dataset of tags. tag mapping analysis was performed using the seqmap tool with one mismatch allowed for ‘unique match’ (a tag which mapped uniquely to only one transcript) and ‘selected match’ (more than one tags matching on a single transcript, wherein […]

PMCID: 5526973
PMID: 28798667
DOI: 10.3389/fncel.2017.00212

[…] of hits across the human genome (grch38.p7). the putative promoter sequences of the same genes were also screened for established foxp2-binding motifs (see ; , ; ). this was done with the aid of seqmap v. 1.0.3 (), without allowing for any mismatch., following others (e.g., ,) we employed the string server (v. 10.0) for the reconstruction of a protein–protein interaction (ppi) network […]

PMCID: 5463065
PMID: 28444881
DOI: 10.1002/cam4.1047

[…] and the robust multichip average (rma) algorithm was performed for background‐adjustment, quantile normalization, and log‐transformation by the r package “affy” . lncrna profiles were achieved by seqmap v1.0.8 on a local computer . briefly, the probe sets of affymetrix hg‐u133 plus 2.0 were retrieved from the affymetrix website ( we then re‐mapped those probes […]

PMCID: 5572453
PMID: 28852597
DOI: 10.7717/peerj.3737

[…] each experiment, samples for b73 leaves were selected, resulting in a high quality, homogeneous dataset of 165 cel files., probeset sequences for the maize affymetrix microarray were aligned using seqmap () to the agpv3.22 transcripts with no mismatches allowed, and probesets whose probe sequences did not align or aligned to transcripts corresponding to more than one locus were discarded. […]

To access a full list of publications, you will need to upgrade to our premium service.

SeqMap institution(s)
Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA; Department of Statistics, Stanford University, Stanford, CA, USA
SeqMap funding source(s)
National Institute of Health (R01HG003903 and U54GM62119).

SeqMap reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SeqMap