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  2. List of sequence alignment software - Wikipedia

    en.wikipedia.org/wiki/List_of_sequence_alignment...

    Linking and profiling sequence alignment data from NCBI-BLAST results with major sequence analysis servers/services: Nucleotide, peptide: 2010 SAM Local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST: Both: Karplus K, Krogh A [15] 1999 SSEARCH Smith-Waterman search, slower but more sensitive than FASTA: Both ...

  3. Sequence profiling tool - Wikipedia

    en.wikipedia.org/wiki/Sequence_profiling_tool

    A sequence profiling tool in bioinformatics is a type of software that presents information related to a genetic sequence, gene name, or keyword input. Such tools generally take a query such as a DNA , RNA , or protein sequence or ‘keyword’ and search one or more databases for information related to that sequence.

  4. List of gene prediction software - Wikipedia

    en.wikipedia.org/wiki/List_of_gene_prediction...

    The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes [8] [9] EuGene: Integrative gene finding: Prokaryotes, Eukaryotes [10] [11] FGENESH: HMM-based gene structure prediction: multiple genes, both chains: Eukaryotes [12] FrameD: Find genes and frameshift in G+C rich prokaryote ...

  5. National Center for Biotechnology Information - Wikipedia

    en.wikipedia.org/wiki/National_Center_for...

    The NCBI assigns a unique identifier (taxonomy ID number) to each species of organism. [5] The NCBI has software tools that are available through web browsers or by FTP. For example, BLAST is a sequence similarity searching program. BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds.

  6. BLAST (biotechnology) - Wikipedia

    en.wikipedia.org/wiki/BLAST_(biotechnology)

    In bioinformatics, BLAST (basic local alignment search tool) [3] is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query ...

  7. List of RNA-Seq bioinformatics tools - Wikipedia

    en.wikipedia.org/wiki/List_of_RNA-Seq...

    fastqp Simple FASTQ quality assessment using Python. Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.

  8. FASTQ format - Wikipedia

    en.wikipedia.org/wiki/FASTQ_format

    Field 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again. Field 4 encodes the quality values for the sequence in Field 2, and must contain the same number of symbols as letters in the sequence. A FASTQ file containing a single sequence might look like this:

  9. BLAT (bioinformatics) - Wikipedia

    en.wikipedia.org/wiki/BLAT_(bioinformatics)

    Once the query sequence is uploaded/pasted into the search field, the user can select various parameters such as which species' genome to target (there are currently over 50 species available) and the assembly version of that genome (for example, the human genome has four assemblies to select from), the query type (i.e. whether the sequence ...

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