J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990). CAS PubMed Google Scholar Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29–W37 (2011). CAS PubMed PubMed Central Google ...
Biophysics Vector alignment search tool (VAST) automated protein structure comparison using special structural elements THE JOHNS HOPKINS UNIVERSITY Stephen H. Bryant TsangHsinyi SteveThe rapid growth in the size of protein structure databases has led to the development of numerous protein structural ...
The Vector Alignment Search Tool (VAST), developed by the Structure Group at the National Center for Biotechnology Information (NCBI), offers a fast and efficient way to perform structural similarity comparisons. The VAST algorithm uses vectors to represent secondary structure elements (SSEs) in ...
Searching for TphC-like proteins was performed by Basic Local Alignment Search Tool (BLAST) in National Center for Biotechnology Information (NCBI) server using the BLAST-P method. Multiple alignment was performed with Clustal omega, and visualised using iTOL75. Taxonomic information for these sequenc...
A structural homology search tool: Foldseek GESAMT viaCCP4 An alignment/visualization tool: ChimeraX1.3+ Perl5and the additonal scripting module: PerlIO::gzip Aria2 Aria2 is a lightweight utility tool that can resume partial downloads. 3DFI uses this tool to download its databases. On Fedora...
ToolURLLanguageInputComments BreakDancer http://breakdancer.sourceforge.net/ Perl, C++ Alignment files Predicting nsertions, deletions, inversions, inter- and intra-chromosomal translocations PEMer http://sv.gersteinlab.org/pemer/ Perl, Python FASTA Using simulation-based error models to call SVs Vari...
To address the phylogenetic relationship of SPIs, the PPs of SBTs, and I9s in fungi, we first performed database searches using the Basic Local Alignment Search Tool for proteins (blastP) to identify SPI-1 homologs in other species. SPI-1 homologs were found across the plant kingdom, ...
Kent WJ: BLAT--the BLAST-like alignment tool. Genome Res. 2002, 12: 656-664. Article PubMed CAS PubMed Central Google Scholar Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, Yoo YJ, Shin JY, Kim HJ, Yavartanoo M, Chang YW, Ha...
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. Article CAS PubMed Google Scholar Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries...
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215 (3): 403-410. Article PubMed Google Scholar Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation...