Seq2Ref specifications


Unique identifier OMICS_20382
Name Seq2Ref
Interface Web user interface
Restrictions to use None
Input data One protein.
Input format TXT, FASTA, gi number
Computer skills Basic
Version 1.2
Stability Stable
Maintained Yes


  • person_outline Nick Grishin
  • person_outline Wenlin Li

Additional information

Publication for Seq2Ref

Seq2Ref citation


HANDS2: accurate assignment of homoeallelic base identity in allopolyploids despite missing data

Sci Rep
PMCID: 4932600
PMID: 27378447
DOI: 10.1038/srep29234

[…] ces were constructed using Ensembl Plants build 1.27 ( containing 41,393 and 59,225 cDNA sequences respectively. The in silico transcriptomic references were obtained using ‘seq2ref’ command in HANDS2, which concatenates the contigs/cDNA sequences such that two consecutive sequences are separated by a gap of 200 (a user specified parameter) Ns (). The B. rapa reference co […]

Seq2Ref institution(s)
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
Seq2Ref funding source(s)
Supported by National Institutes of Health (GM094575) and the Welch Foundation (I-1505).

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