Search Results for "blast" - Page 2
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Showing 113 open source projects for "blast"
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Train ML Models With SQL You Already KnowBuild and deploy ML models using familiar SQL. Automate data prep with built-in Gemini. Query 1 TB and store 10 GB free monthly.
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Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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idwtree
Assigns orthologs using a phylogenetic tree
...Use idwtree to assign BLAST hits to ortholog groups -
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... * After setting the CodeIgniter framework, unzip it under the default home directory. The database is based on Maria DB (mysql). Download the schema and import it into the DB. Each species you want to analyze needs blast results. Fit the fields to match the schema and it will work.
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pydictor
powerful and useful hacker dictionary builder for a brute-force attack
A powerful and useful hacker dictionary builder for a brute-force attack. You can use pydictor to generate a general blast wordlist, a custom wordlist based on Web content, a social engineering wordlist, and so on; You can use the pydictor built-in tool to safe delete, merge, unique, merge and unique, count word frequency to filter the wordlist, besides, you also can specify your wordlist and use '-tool handler' to filter your wordlist. You can generate highly customized and complex wordlists by modifying multiple configuration files, adding your own dictionary, using leet mode, filter by length, char occur times, types of different char, regex, and even add customized encode scripts in /lib/encode/ folder, add your own plugin script in /plugins/ folder, add your own tool script in /tools/ folder. -
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weinberg-overcluster2
Cluster subsequences of intergenic regions
overcluster2 is a program to cluster subsequences of InterGenic Regions (IGRs). It clusters these subsequences based on the output of BLAST comparisons of the IGRs. overcluster2 has been used as part of a method to discover novel non-coding RNA classes. overcluster2 was written by Zasha Weinberg. The basic method was one of the methods described here: https://www.ncbi.nlm.nih.gov/pubmed/19340921 An example of the use of overcluster2 to find non-coding RNAs is here: https://www.ncbi.nlm.nih.gov/pubmed/20230605 -
Our Free Plans just got better! | Auth0You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.
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Hamstr
A tool for directed ortholog search in ESTs and proteins
...The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with novel sequences from the search taxon. -
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AmpliMethProfiler
CpG methylation analysis of amplicons from bisulfite sequencing
...Specifically, ampliMethProfiler provides an easy and user friendly way to extract and analyze the epiallelic composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is written in python language and requires a local installation of BLAST and QIIME tools. It can be run on Linux and OS X platforms. HOW TO CITE US: "ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons". Scala G., et al. BMC Bioinformatics (2016) 17:484, DOI: 10.1186/s12859-016-1380-3 -
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Kinannote
Protein Kinase Identification and Classification
...If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes. Kinannote runs on a unix command line and depends on local hmmer 2 and Blast 2.24 installations. Citing Kinannote: Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily Jonathan M. Goldberg; Allison Griggs; Janet L. Smith; Brian Haas; Jennifer Wortman; Qiandong Zeng Bioinformatics 2013; doi: 10.1093/bioinformatics/btt419 http: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full pdf: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full.pdf+html -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
...Therefore, identification conserve and novel miRNA and their target genes in model and new sequenced species are inevitable. MITP is designed to identify miRNA easily and faster based on sequence mapping result from any mapping software which producing SAM format output result, blast result (default output result) or blat result (default output result). The program provide a step praramter (8 steps) which can allow running program from any step and finishing all remaining steps. You also can run step by step using each step program. Please run these step programs at the same directory for running main program MITP.pl. ... -
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Development page for MultiGeneBlast, a combined blast search tool for identifying homologs of multigene modules in genomes.
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Error to trace to log to deploy. One click. No SSH.AppSignal links every error to the trace, the trace to the log, the log to the deploy that shipped it.
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Genix: Bacterial Genome Annotation Pipel
A automated annotation pipeline for bacteria / archea genomes
Genix is an online automated pipeline for bacterial genome annotation that integrates the programs Prodigal, BLAST, RNAmmer, tRNAscan-SE, INFERNAL, ARAGORN and HMMER, and the databases Uniprot, Antifam and Rfam. -
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Protospacer Workbench
CRISPR/Cas9 guide-RNA design
...The main difficulty arises from the need to identify potential off-targets that may be quite different from the intended target. Current online tools for guide-RNA design provide a user friendly interface to sequence mapping software such as Bowtie or BLAST. However, while fast, these mapping algorithms were not designed with a high tolerance to error, a feature critical to determining potential off-targets. Where online tools fail, offline tools succeed. However, offline tools require knowledge of the command line which few, who employ CRISPR, have. Protospacer Workbench aims to bridge the gap between online and offline guide-RNA design. ... -
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SUPER Ninja Robot
3D Vertical Platforming!
This is SUPER Ninja Robot! 3D Vertical Platformer where you blast your way through each level! -
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SimplyTheBlast
Blast query sequences on a set of fasta formatted genomes
SimplyTheBlast: a small perl tool to build genes presence/absence matrices over a set of Fasta formatted genomes. This code requires: Bio::SeqIO; Bio::Perl; Bio::Tools::Run::StandAloneBlast; Bio::Seq; Bio::Tools::Blast; Bio::DB::GenBank; Bio::DB::WebDBSeqI; and BLAST 2.2.28 (blastall and formatcmd) installed and reachable from your command line Usage: perl SimplyTheBlast-Align.pl <fasta formatted seeds file> <path to genomes folder> <Alignment length threshold in %> <Alignment identity threshold in %> OR Usage: perl SimplyTheBlast-Evalue.pl <fasta formatted seeds file> <path to genomes folder> <Evalue threshold> Genomes files names must end with *.faa Output files: TABULAR_FBH_OUTPUT.xls is an Excel readable file with the identifier of the best hits found TABULAR_FBH_OUTPUT.csv is a file with the number of the best hits found query_n* files are fasta formatted files with the sequences of the best hits found bugs /comments: marco.fondi@unifi.it -
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mitoMaker
mitoMaker - a mitochondria assembly and annotation script
mitoMaker is a pipeline script developed to simplify the assembly and automatic annotation of mitochondrial genomes, based on raw NGS reads and an optional target reference. mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others. General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches a target mitochondrial genome given. 2-searches for all mitochondrial gene features and circularization. 3-stores the best result found. 4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps. 5-annotates the best assembly, identifying the start and end position of each and every feature. 6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile). -
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TUIT
Taxonomic Unit Identification Tool
...Read our paper in Biotechniques: http://www.ncbi.nlm.nih.gov/pubmed/24502797 Taxonomic Unit Identification Tool (TUIT) is a free open source platform-independent software, designed specifically to facilitate taxonomic annotation of nucleotide sequences via BLAST homology search against the NCBI databases. TUIT is immediately applicable for both to 16S microboime studies as well as for taxonomic classification of the nucleotide reads. Please see the project's Wiki page. -
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reciprocal blast for windows
Pipeline for automatic reciprocal blast
Set of python3 scripts and windows batch scripts which use extensively NCBI Blast+ package and BioPython module to perform algorithm known as reciprocal blast. README: https://sourceforge.net/projects/reciprocalblastwin32/files/ -
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simulate_pcr
PCR target prediction software
...The PCR amplicon simulation code also annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons. It is an open source command line Perl script called simulate_PCR.pl that calls the BLAST (Altschul, et al., 1990) programs makeblastdb, blastn, and blastdbcmd, and the NCBI efetch utility (http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi). -
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GBLASTN
G-BLASTN is a GPU-accelerated nucleotide alignment tool.
G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. G-BLASTN can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. -
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NGSbinningpytools
Python tools for binning NGS scaffolds to various genomes.
Next generation sequencing has opened new avenues for sequencing prokaryotes which were difficult or either impossible to culture. Now, it is possible to sequence all organisms present in a metagenomic community. However, a critical problem is to determine the host organism for each genomic fragment present in the dataset. This project provides the computational tools for assigning the organismal identity for each genomic scaffold in the given dataset. For more detailed documentation... -
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BLAST_FDR
BLAST_FDR and PSI-BLAST_FDR are variants of BLAST and PSI-BLAST
BLAST_FDR and PSI-BLAST_FDR are variants of BLAST and PSI-BLAST. Instead of using BLAST and PSI-BLAST's uniform E-value threshold criterion to determine which sequences to include, BLAST_FDR and PSI-BLAST_FDR utilize a false discovery rate (FDR) method. -
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...Under wEMBOSS each user has a private workspace (UNIX home directory) on the server, where he can permanently store his data and organize them in projects. The companion suite wrappers4EMBOSS allows to integrate under EMBOSS a number of popular bioinformatic software suites as BLAST, CLUSTAL and MRS.
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provean
Predicting the functional effect of protein sequence variations
PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. The prediction is based on the change, caused by a variation, in the similarity of query sequence to closely related sequences collected through BLAST. -
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SeqSelector
Tools to select sequences for capture enrichment of next-gen libraries
...We suggest a workflow in which genes of interest are first identified from previous studies and publicly available datasets of functional gene annotation. Once a list of candidate genes has been identified, their sequences are selected from the reference genome. These sequences are used as a query during a BLAST search of the unannotated genome of a non-model species, and then the corresponding sequences are returned, which can be used to design baits for hybridization-based sequence capture.
