Search Results for "blast"

Code Review Graph is a local-first code intelligence tool that builds a persistent structural map of a software repository. It parses source files with Tree-sitter and stores functions, classes, imports, calls, inheritance, and test relationships in a SQLite graph. When code changes, blast-radius analysis identifies the callers, dependents, and tests most likely to be affected. AI coding assistants can query this focused context through MCP instead of repeatedly scanning an entire codebase. Incremental indexing reparses only changed files and their relevant dependencies, making it practical for large repositories and monorepos. ...

KimBlast GUI formats and indexes Fasta databases for Blast, performs Blast searches and analyzes results. Python 3.x version. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/kimblast3/code/ci/default/tree/README.md

...I was given the honor to demonstrate software engineering at an event to help introduce young women to the various fields of engineering. This project was made just for the occasion! I had a blast making it and I hope everyone enjoys this FOSS just as much. The simple design and well-commented code is a great example of turning an everyday object into a shareable program for others to enjoy. Requires Python 3.7 and Pygame 1.9.6. These are FREE: Python Download: https://www.python.org/downloads/ Python/Pygame install YouTube tutorial: https://www.youtube.com/watch?...

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.

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).

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...

...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.

NOW HOSTED ON GITHUB: https://github.com/kylebittinger/brocc Old releases are kept here for archival purposes.

metaProt is a python pipeline to analyze and extract data from protein sequences found in metagenomic projects. It integrates several existing tools (HMMer, Pepstats, Blast...) to be used against custom databases. Please, read the README.txt file to find more about this.

NumericalFISH is a bioinformatics graphical tool for easy analysis of BLAST or BLAT results, especially aimed at the study of duplications or segmental duplications.

FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra

Text2Genome is a set of scripts to extract nucleotide sequences from scientific articles and to map them to genomes and genes using a local alignment algorithm (BLAST/BLAT)