scholarly journals BLAST output visualization in the new sequencing era

2013 ◽  
Vol 15 (4) ◽  
pp. 484-503 ◽  
Author(s):  
R. S. Neumann ◽  
S. Kumar ◽  
K. Shalchian-Tabrizi
Keyword(s):  
Blast Output

scholarly journals Decona: From demultiplexing to consensus for Nanopore amplicon data

2021 ◽  
Vol 4 ◽  
Author(s):  
Saskia Oosterbroek ◽  
Karlijn Doorenspleet ◽  
Reindert Nijland ◽  
Lara Jansen
Keyword(s):  
Sequence Data ◽  
Variant Calling ◽  
Environmental Dna ◽  
Laptop Computer ◽  
Consensus Sequences ◽  
Sequencing Errors ◽  
Blast Output ◽  
Command Line Tool ◽  
Microbial Symbionts ◽  
User Friendly

Sequencing of long amplicons is one of the major benefits of Nanopore technologies, as it allows for reads much longer than Illumina. One of the major challenges for the analysis of these long Nanopore reads is the relatively high error rate. Sequencing errors are generally corrected by consensus generation and polishing. This is still a challenge for mixed samples such as metabarcoding environmental DNA, bulk DNA, mixed amplicon PCR’s and contaminated samples because sequence data would have to be clustered before consensus generation. To this end, we developed Decona (https://github.com/Saskia-Oosterbroek/decona), a command line tool that creates consensus sequences from mixed (metabarcoding) samples using a single command. Decona uses the CD-hit algorithm to cluster reads after demultiplexing (qcat) and filtering (NanoFilt). The sequences in each cluster are subsequently aligned (Minimap2), consensus sequences are generated (Racon) and finally polished (Medaka). Variant calling of the clusters (Medaka) is optional. With the integration of the BLAST+ application Decona does not only generate consensus sequences but also produces BLAST output if desired. The program can be used on a laptop computer making it suitable for use under field conditions. Amplicon data ranging from 300-7500 nucleotides was successfully processed by Decona, creating consensus sequences reaching over 99,9% read identity. This included fish datasets (environmental DNA from filtered water) from a curated aquarium, vertebrate datasets that were contaminated with human sequences and separating sponge sequences from their countless microbial symbionts. Decona considerably simplifies and speeds up post sequencing processes, providing consensus sequences and BLAST output through a single command. Classifying consensus sequences instead of raw sequences improves classification accuracy and drastically decreases the amount of sequences that need to be classified. Overall it is a user friendly option for researchers with limited knowledge of script based data processing.

scholarly journals Multi-query sequence BLAST output examination with MuSeqBox

2001 ◽  
Vol 17 (8) ◽  
pp. 744-745 ◽  
Author(s):  
L. Xing ◽  
V. Brendel
Keyword(s):  
Query Sequence ◽  
Blast Output

scholarly journals BOV – a web-based BLAST output visualization tool

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 414 ◽  
Author(s):  
Rajesh Gollapudi ◽  
Kashi Revanna ◽  
Chris Hemmerich ◽  
Sarah Schaack ◽  
Qunfeng Dong
Keyword(s):  
Visualization Tool ◽  
Web Based ◽  
Blast Output

scholarly journals AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts

2005 ◽  
Vol 33 (Web Server) ◽  
pp. W665-W668 ◽  
Author(s):  
G. Lavorgna ◽  
R. Triunfo ◽  
F. Santoni ◽  
U. Orfanelli ◽  
S. Noci ◽  
...  
Keyword(s):  
Antisense Transcripts ◽  
Blast Output

Btab—a Blast output parser

1992 ◽  
Vol 8 (6) ◽  
pp. 601-602 ◽  
Author(s):  
M. Dubnick
Keyword(s):  
Blast Output

scholarly journals AntiHunter: searching BLAST output for EST antisense transcripts

2004 ◽  
Vol 20 (4) ◽  
pp. 583-585 ◽  
Author(s):  
G. Lavorgna ◽  
L. Sessa ◽  
A. Guffanti ◽  
L. Lassandro ◽  
G. Casari
Keyword(s):  
Antisense Transcripts ◽  
Blast Output

rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output

2021 ◽  
Author(s):  
Marek Schwarz ◽  
Jiří Vohradský ◽  
Josef Pánek
Keyword(s):  
Web Service ◽  
Web Server ◽  
Command Line ◽  
Interactive Analysis ◽  
Blast Output ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Ncbi Blast ◽  
The Web

Abstract Summary We present a web service for improving characterization of non-coding RNAs (ncRNAs) from NCBI BLAST outputs, based on a command-line application rboAnalyzer. Briefly, the application extends subject sequences of selected high scoring pairs (HSPs) in BLAST output to their plausible full length, and predicts their homology and secondary structures. The aim of the application is to aid to characterize subject RNAs in HSPs that come uncharacterized in BLAST output. The main advantages of the web-server are easy use and interactive analysis with search, filtering and data export options. Availability and implementation The web server is freely available at rboanalyzer.elixir-czech.cz. The website frontend is implemented in Elm, while backend is implemented in Python and served by Apache.

scholarly journals BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments

2004 ◽  
Vol 20 (12) ◽  
pp. 1968-1970 ◽  
Author(s):  
M. Suyama ◽  
D. Torrents ◽  
P. Bork
Keyword(s):  
Blast Output
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