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  • Abhi published a blog post Tools for Sequence translation ! 1366 days ago
    A core element in the downstream analysis for RNA-seq data involves the translation of assembled sequences into their corresponding amino acid sequences, and on the nucleotide level into the protein coding sequences (CDS) not containing any...
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    • LEGE 1242 days ago

      Sequence translation is the process of converting a DNA or RNA sequence into its corresponding protein sequence. This is an important step in the analysis of genomic and transcriptomic data. There are several tools available for sequence translation, including:

      1. ExPASy Translate Tool: This is a web-based tool that allows users to translate a DNA sequence into its corresponding protein sequence. It supports several genetic codes and can handle multiple sequences at once.

      2. EMBOSS Transeq: This is a command-line tool that can translate nucleotide sequences into amino acid sequences. It supports several genetic codes and can also perform reverse translation (i.e., convert a protein sequence into its corresponding nucleotide sequence).

      3. BioPython: This is a Python library that provides several tools for bioinformatics analysis, including sequence translation. It supports several genetic codes and provides functions for translating DNA or RNA sequences into protein sequences.

      4. SeqKit: This is a command-line tool that can perform several sequence manipulations, including sequence translation. It supports several genetic codes and can handle multiple sequences at once.

      5. CLC Sequence Viewer: This is a desktop application that provides several tools for sequence analysis, including sequence translation. It supports several genetic codes and provides a user-friendly interface for performing the analysis.

      These are just a few examples of the many tools available for sequence translation. The choice of tool depends on the specific requirements of the user, including the input format, the genetic code used, and the type of output required.

  • Abhi posted a new ad in the Opportunity PhD positions on integrative omics and phylogenomics 1386 days ago
  • Abhi created a new bio-script Perl script to read the next line of a file ! 1387 days ago
  • Abhi bookmarked Visualise blast results ! 1394 days ago
    Kablammo helps you create interactive visualizations of BLAST results from your web browser. Find your most interesting alignments, list detailed parameters for each, and export a publication-ready vector image, all without installing any...
  • Abhi published a blog post Must read paper and books in evolution biology ! 1399 days ago
    Books and research paper to read
  • Abhi published a blog post Useful link to teach evolution ! 1399 days ago
    Mimicry and other resources
  • Abhi created a page Read Simulators 1405 days ago
    Short Read Simulators With the popularity of next-generation sequencing (NGS) technologies, many NGS read simulators have been developed. Currently, many of the popular short read simulators are designed to simulate reads mimicking many Illumina,...
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    • BioStar 1237 days ago

      There are several tools available for short read simulators that are widely used in bioinformatics research. Here are some of them:

      1. ART: The ART (short for Artificial Read Simulator) is a popular tool for generating synthetic reads based on sequencing technologies such as Illumina, SOLiD, and 454. It is a versatile tool that allows users to simulate reads with different error rates, read lengths, and insert sizes. The ART is open-source and available for free download.

      2. wgsim: wgsim is another widely used short read simulator that generates synthetic reads based on the whole genome sequencing technology. It can simulate reads with different read lengths, error rates, and coverage levels. The wgsim tool is also open-source and available for free download.

      3. PIRS: PIRS (short for Profile-based Illumina pair-end Reads Simulator) is a short read simulator that uses a profile-based approach to generate synthetic reads. It can simulate reads with different sequencing technologies, including Illumina, Ion Torrent, and PacBio. PIRS allows users to customize different sequencing parameters, such as error rates, read lengths, and insert sizes.

      4. SimSeq: SimSeq is a Python-based short read simulator that allows users to simulate reads from different sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. It can also simulate different types of sequencing errors, such as substitution, insertion, and deletion errors.

      5. dwgsim: dwgsim is a short read simulator that can generate synthetic reads from whole genome sequencing data. It is designed to simulate reads from large genomes and can handle complex genome structures, such as translocations and inversions.

      These are just a few examples of the many short read simulators available for bioinformatics research. The choice of the simulator depends on the specific research question and the type of sequencing technology used in the study.

  •   The abundance of a species in a dataset is considered as the fraction of reads that belong to that species. For example, if there is a dataset with 10,000,000 reads and 1,000,000 of them belong to E. coli, then the abundance...
  • Abhi commented on a bookmark CovCal: Coverage / Read Count Calculator 1405 days ago
    Sequencing coverage is defined as the average number of reads that covers each base of the reference genome. Estimating the sequencing coverage is very important when you are simulating datasets. The coverage equation is defined as...
  • Abhi bookmarked Covid Spectrum ! 1409 days ago
    https://cov-spectrum.org/explore/World/AllSamples/ CoV-Spectrum supports a wide range of search queries. The following sections presents search options of the basic search bar. For information on the advanced search
  • Abhi bookmarked Covid Spectrum ! 1409 days ago
    https://cov-spectrum.org/explore/World/AllSamples/ CoV-Spectrum supports a wide range of search queries. The following sections presents search options of the basic search bar. For information on the advanced search
  • Abhi bookmarked Covid Spectrum ! 1409 days ago
    https://cov-spectrum.org/explore/World/AllSamples/
  • Abhi bookmarked Executing Snakemake 1409 days ago
    This part of the documentation describes the snakemake executable. Snakemake is primarily a command-line tool, so the snakemake executable is the primary way to execute, debug, and visualize...
  • Abhi created a new bio-script Extract the mapped and unmapped reads ! 1412 days ago
  • Jit commented on a page titled Phylogenetic for Bioinformatics 1412 days ago
    Nice evolutionary distance caculation methods @ https://www.cs.rice.edu/~nakhleh/COMP571/Slides/Phylogenetics-DistanceMethods-Full.pdf
  • Jit commented on a page titled Phylogenetic for Bioinformatics 1413 days ago
    Nice tutorial https://www.zoology.ubc.ca/~bio336/Bio336/Lectures/Lecture14/Overheads.html
  • Jit created a new bio-script Blast short sequences ! 1414 days ago
  • gfastats is a single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation. gfastats also allows seamless fasta<>fastq<>gfa[.gz]...
  • Abhi commented on a page titled Elgg Installation steps ! 1428 days ago
    Useful for debugging  https://stackoverflow.com/questions/43094726/your-password-does-not-satisfy-the-current-policy-requirements https://elgg.org/discussion/view/1945994/elgg-requires-the-php-extension-gd
  • Abhi created a page Elgg Installation steps ! 1428 days ago
    Elgg is an open source social networking engine that allows the creation of social environments such as campus social networks and internal collaborative platforms for organizations. Elgg offers a number of social networking features including...
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