PMID- 19514837
OWN - NLM
STAT- MEDLINE
DCOM- 20091014
LR  - 20090611
IS  - 1557-8100 (Electronic)
IS  - 1536-2310 (Linking)
VI  - 13
IP  - 3
DP  - 2009 Jun
TI  - Seq-SNPing: multiple-alignment tool for SNP discovery, SNP ID identification, and 
      RFLP genotyping.
PG  - 253-60
LID - 10.1089/omi.2008.0058 [doi]
AB  - Many sequence-alignment tools were developed to discover single nucleotide 
      polymorphisms (SNPs) derived from resequencing in genomic regions. Whether an 
      identified SNP is indeed a novel SNP or is already contained in dbSNP is often 
      difficult to answer. Here, we describe a freely available software, Seq-SNPing, 
      which is a Java-based software for SNP discovery, and ID identification and 
      editing and visualizating of sequence alignments. It is easy to use, fast, and 
      provides an accurate method for searching and organizing SNP IDs from multiple 
      sequence inputs, thereby greatly facilitating genetic studies. Seq-SNPing 
      provides SNP identification by selecting any range of unaligned or aligned 
      sequences in sequences that are similar. SNP IDs in the National Center for 
      Biotechnology Information (NCBI) or user-defined SNPs within a selected sequence 
      can be identified by Seq-SNPing. Information needed for SNP-RFLP (restriction 
      fragment length polymorphism) genotyping is provided, such as SNP-REs 
      (restriction enzymes), the sequence trimmer, sequence finder, BLAST (Basic Local 
      Alignment Search Tool), SNP-BLAST, UCSC BLAT (BLAST-like alignment tool), RE 
      mining, antisequencer (Anti-seq), and T(m) (melting temperature)/GC% of selected 
      sequence. The thresholds for SNP calling are adjustable by selecting the height 
      of the peak for each nucleotide representative curve in the chromatogram. 
      Therefore, Seq-SNPing can discover SNPs and identify SNP IDs in both sequence 
      text and chromatogram files in a fast and reliable way. The software is fully 
      compatible with Microsoft Windows. The program and user manual are available at 
      http://bio.kuas.edu.tw/Seq-SNPing for download.
FAU - Chang, Hsueh-Wei
AU  - Chang HW
AD  - Department of Biomedical Science and Environmental Biology, Kaohsiung Medical 
      University, Kaohsiung, Taiwan, ROC.
FAU - Chuang, Li-Yeh
AU  - Chuang LY
FAU - Cheng, Yu-Huei
AU  - Cheng YH
FAU - Ho, Chang-Hsuan
AU  - Ho CH
FAU - Wen, Cheng-Hao
AU  - Wen CH
FAU - Yang, Cheng-Hong
AU  - Yang CH
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - OMICS
JT  - Omics : a journal of integrative biology
JID - 101131135
SB  - IM
MH  - Base Sequence
MH  - Databases, Genetic
MH  - *Genotype
MH  - Humans
MH  - Molecular Sequence Data
MH  - *Polymorphism, Restriction Fragment Length
MH  - *Polymorphism, Single Nucleotide
MH  - Sequence Alignment/*methods
MH  - Sequence Analysis, DNA/*methods
MH  - *Software
MH  - User-Computer Interface
EDAT- 2009/06/12 09:00
MHDA- 2009/10/15 06:00
CRDT- 2009/06/12 09:00
PHST- 2009/06/12 09:00 [entrez]
PHST- 2009/06/12 09:00 [pubmed]
PHST- 2009/10/15 06:00 [medline]
AID - 10.1089/omi.2008.0058 [doi]
PST - ppublish
SO  - OMICS. 2009 Jun;13(3):253-60. doi: 10.1089/omi.2008.0058.