Splign protocols

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Splign specifications


Unique identifier OMICS_17368
Name Splign
Interface Web user interface
Restrictions to use None
Input data An Amino acid substitution score matrix.
Input format FASTA
Output data Contains all pairwise alignments.
Output format SRSPAIR, FASTA
Programming languages C++
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Yuri Kapustin <>

Publication for Splign

Splign in pipelines

PMCID: 5826354
PMID: 29515615
DOI: 10.3389/fpls.2018.00216

[…] sequencing and assembling a full coding sequences of barley homologs. after that, the barley coding sequence was aligned with the genomic sequence of the rice homolog using blastn algorithm or splign (http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi) what allowed to predict exon/intron putative borders in the barley gene and design primers for amplification of intron regions. […]

PMCID: 5433004
PMID: 28506210
DOI: 10.1186/s12863-017-0506-6

[…] the genomic sequences were identified from potato genome sequencing consortium database (http://potatogenome.net/index.php/main_page). the gene structures (exon and intron) were analyzed with splign (http://www.ncbi.nlm.nih.gov/sutils/splign) []. the promoter sequences were identified about 2 kb upstream of the transcription start site of each gene, and the abiotic stress-associated […]

PMCID: 5489561
PMID: 28706522
DOI: 10.3389/fpls.2017.01034

[…] were predicted by aligning them to the then available banana genomic sequence (accession number: caic01023700 positions 70772 to 76310) from m. acuminata genotype ‘dh pahang’ using the program splign ()., secondary structures of proteins were predicted using the original garnier osguthorpe robson algorithm (gor i) provided by the european molecular biology open software suite (emboss) […]

PMCID: 5629197
PMID: 28983085
DOI: 10.1038/s41598-017-12725-5

[…] nucleotide sequences to the felis catus reference genome (assembly felis_catus_8.0). gene usage was determined by mapping clone sequences to the feline reference chromosomes using ncbi blast and splign alignment tools (nc_018728 for igh clones; nc_018734 for igl clones; nc_018725.2 for igk clones) (https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi)., phylogenetic analysis of 71 clone […]

PMCID: 4069619
PMID: 24803641
DOI: 10.1093/molbev/msu135

[…] were significantly overrepresented. exonic and intronic regions were determined by aligning the cdna and gdna genomic resources outlined in and identfying putative exon–intron boundaries using splign (). synonymous and nonsynonymous substitutions were identified from the snp sequences using snap v1.1.1 ()., estimations of allele frequencies, observed (ho) and expected (he) heterozygosity […]

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Splign in publications

PMCID: 5942844
PMID: 29702654
DOI: 10.1371/journal.pntd.0006428

[…] base pairs to that seen in fertilized fasciola eggs (expression levels at this stage = 1, hence log2 = 0)., exon-intron boundaries of the final extended fhtaut sequence were detected using the splign web interface (https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi) []. the visualization of exons and introns organization in the genome was done by exon-intron graphic maker […]

PMCID: 5884551
PMID: 29570707
DOI: 10.1371/journal.pgen.1007272

[…] 0.9—outfiltermultimapnmax 1) against the public genome (bioproject: prjna72441) that we had annotated before by aligning the above-mentioned naked mole-rat transcriptome reference using blat [] and splign []. rat reads were aligned against the mentioned refseq reference using bwa aln [] (-n 2 -o 0 -e 0 -o 1000 -e 1000). read data and counts were deposited as geo (gene expression omnibus) series […]

PMCID: 5855819
PMID: 29462998
DOI: 10.3390/ijms19020597

[…] isolation of both oeaox1 gene members: oeaox1a with 2215 bp and oeaox1d with 2054 bp length (from start to stop codon). to identify gene structure, genomic and transcript sequences were used at the splign software. a four exons structure showing size conservation at the three last exons (exon 2: 129, exon 3: 489 and exon 4: 57 bp), interrupted by three size variable introns, was identified […]

PMCID: 5833675
PMID: 29449584
DOI: 10.1038/s41419-018-0301-y

[…] 0.5 mm glutamax). ipsc neural conversion was monitored by microscopic inspection of cells., refseq sequences were downloaded on june 25, 2014, and transcript models identified using gmap and splign alignments to ucsc mm10. refseq cds annotations were used to determine coding regions. candidate guide 19-mers with an ngg pam that were entirely contained in a cds (including the pam) […]

PMCID: 5825161
PMID: 29432451
DOI: 10.1371/journal.pntd.0006235

[…] confirmation of the presence of micro-exons was obtained by examining the gene structure, based on alignment of the transcript sequence with the corresponding s. japonicum genome segment, using the splign program available at the ncbi website. known and putative meg products were assessed for the presence of highly disordered regions, secondary structure and a long stretch of amino acids (n […]

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Splign institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

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