SeqMap: mapping massive amount of oligonucleotides to the genome

By Hui Jiang, Wing Hung Wong. Bioinform., 2008

502 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0fdf599351f7358a16e59be57d9f90aee7fa76b5

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Artificial Intelligence

1. Heng Li
2. Jun Zhang
3. A. Badr
4. R. Chiodini
5. Genfa Zhang
6. Nils Homer
7. Hui Jiang
8. Wing Hung Wong

In Molecular Biology

1. Lei S. Qi
2. Heng Li
3. Nils Homer
4. Jun Zhang
5. A. Badr
6. R. Chiodini
7. Genfa Zhang
8. Luke A. Gilbert

Citations in the corpus

• CRISPR interference (CRISPRi) for sequence-specific control of gene expression (2013, methodology): “▲ CRITICAL STEP To compute the off-targets of large numbers of sgRNAs, computational algorithms for genome mapping of the short nucleotides should be used, such as Seqmap (http://www-personal.umich.edu/~jianghui/seqmap/) 50 .”
• Machine learning-based integration develops an immune-derived lncRNA signature for improving outcomes in colorectal cancer (2022, methodology): “We reannotated probe sets of the GPL570 array for genes by mapping all probes to the human genome (hg38) using SeqMap 39 and then obtained 3439 lncRNA and 17046 protein-coding genes.”
• The impact of next-generation sequencing on genomics (2011, methodology): “Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”
• A survey of sequence alignment algorithms for next-generation sequencing (2010, methodology): “small gaps at each read positions [17, 18].”
• Statistical inferences for isoform expression in RNA-Seq (2009, methodology): “Genes that have RPKMs between 1 and 100 are considered to be moderately expressed. mouse genome (mm9, NCBI Build 37) and all the sequencing reads are mapped to the reference sequences using SeqMap, a short sequence mapping Tool (Jiang and Wong, 2008).”
• sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites (2014, methodology): “SeqMap is a tool that can map large amounts of short oligonucleotides to the genome at very high speed, making it suitable for use as an off-target predictor [30].”