SeqMap protocols

SeqMap computational protocol

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


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  • 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 [51]., so far, no pirna reference dataset for medaka […]

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 [25] using seqmap [42] for the 36-cycle reads, or to blat [43] for the 48-cycle reads, because of the high rate of cis-splicing. because of the highly polymorphic genic features of this organism [44], we used […]

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).

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