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  2. Conserved signature indels - Wikipedia

    en.wikipedia.org/wiki/Conserved_signature_indels

    Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. [1] [2] CSIs, brought about by rare genetic changes, provide useful phylogenetic markers that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability.

  3. 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.

  4. Sequence alignment - Wikipedia

    en.wikipedia.org/wiki/Sequence_alignment

    Motif finding, also known as profile analysis, constructs global multiple sequence alignments that attempt to align short conserved sequence motifs among the sequences in the query set. This is usually done by first constructing a general global multiple sequence alignment, after which the highly conserved regions are isolated and used to ...

  5. Conserved sequence - Wikipedia

    en.wikipedia.org/wiki/Conserved_sequence

    Conserved sequences with a known function, such as protein domains, can also be used to predict the function of a sequence. Databases of conserved protein domains such as Pfam and the Conserved Domain Database can be used to annotate functional domains in predicted protein coding genes.

  6. Multiple sequence alignment - Wikipedia

    en.wikipedia.org/wiki/Multiple_sequence_alignment

    The other is that conserved regions known to be functionally important can be found. This makes it possible for multiple sequence alignments to be used to analyze and find evolutionary relationships through homology between sequences. Point mutations and insertion or deletion events (called indels) can be detected.

  7. Gene prediction - Wikipedia

    en.wikipedia.org/wiki/Gene_prediction

    Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.

  8. BLOSUM - Wikipedia

    en.wikipedia.org/wiki/BLOSUM

    The BLOSUM62 matrix, the amino acids have been grouped and coloured based on Margaret Dayhoff's classification scheme. Positive and zero values have been highlighted. In bioinformatics, the BLOSUM (BLOcks SUbstitution Matrix) matrix is a substitution matrix used for sequence alignment of proteins.

  9. Sequence homology - Wikipedia

    en.wikipedia.org/wiki/Sequence_homology

    Bottom: in a separate species , a gene has a similar function (histone-like nucleoid-structuring protein) but has a separate evolutionary origin and so is an analog. Sequence homology is the biological homology between DNA , RNA , or protein sequences , defined in terms of shared ancestry in the evolutionary history of life .