vimalinx/bio-agent - Seite 3

download-sequence

Use when downloading NCBI ASN.1 biological sequence archive divisions such as BCT, PLN, or VRL into the current directory.

Quellsprache: Englisch

ds2pme

Use when converting PubMed `DocumentSummary` XML into `Pubmed-entry` ASN.1 text, or into the intermediate XML form before final ASN.1 flattening.

Quellsprache: Englisch

dustmasker

Use when masking low-complexity regions in nucleotide sequences using the Symmetric DUST algorithm before BLAST searches or other sequence analyses.

Quellsprache: Englisch

easel

Use when invoking the top-level `easel` dispatcher to discover or run Easel sequence-analysis subcommands from the HMMER toolchain.

Quellsprache: Englisch

ecollect

Use when collecting sorted UID lists from EDirect query sources such as PubMed queries, explicit IDs, WebEnv history state, or input files.

Quellsprache: Englisch

ecommon-sh

Use when auditing or reusing the shared EDirect shell functions that other Entrez Direct wrapper scripts source internally.

Quellsprache: Englisch

efetch

Use when you need to fetch records or data from NCBI Entrez databases (PubMed, nucleotide, protein, gene, SRA, etc.) by ID or accession

Quellsprache: Englisch

efilter

Use when filtering Entrez search results by date, organism, publication type, sequence features, or other database-specific criteria in bioinformatics pipelines.

Quellsprache: Englisch

einfo

Use when you need to discover available NCBI Entrez databases, explore searchable fields within a specific database, or identify cross-database links for building EDirect queries.

Quellsprache: Englisch

elink

Use when you need to navigate relationships between records in NCBI Entrez databases, find related articles, track citations, or link records across different databases such as PubMed to Protein.

Quellsprache: Englisch

epost

Use when you need to post unique identifiers or accession numbers to NCBI Entrez databases for subsequent retrieval operations

Quellsprache: Englisch

esample

Use when printing canned sample NCBI XML, JSON, flatfile, or GFF documents for testing, parser development, or xtract query prototyping.

Quellsprache: Englisch

esearch

Use when searching NCBI Entrez databases (pubmed, gene, protein, nuccore, snp, geoprofiles) with query strings and field qualifiers to retrieve record UIDs for downstream processing.

Quellsprache: Englisch

esl-afetch

Use when retrieving specific multiple sequence alignments from an MSA file by name, or when indexing MSA files for faster access.

Quellsprache: Englisch

esl-alimanip

Use when manipulating multiple sequence alignment files using Easel tools from HMMER.

Quellsprache: Englisch

esl-alimap

Use when comparing or mapping two multiple sequence alignments in Stockholm format to analyze their overlap or relationship.

Quellsprache: Englisch

esl-alimask

Use when you need to mask columns in a multiple sequence alignment using gap frequencies, posterior probabilities, external mask files, or the RF annotation, or to truncate alignments to specific coordinate ranges.

Quellsprache: Englisch

esl-alimerge

Use when merging multiple sequence alignment files in Stockholm or Pfam format into a single alignment.

Quellsprache: Englisch

esl-alipid

Use when calculating pairwise percent identities from multiple sequence alignments in FASTA or Stockholm format.

Quellsprache: Englisch

esl-alirev

Use when you need to reverse sequences in a multiple sequence alignment file. Part of the Easel toolkit distributed with HMMER.

Quellsprache: Englisch

esl-alistat

Use when working with alignment files and needing statistics from HMMER's Easel toolkit.

Quellsprache: Englisch

esl-compalign

Use when comparing a test multiple sequence alignment against a trusted reference alignment to compute accuracy. Requires Stockholm format files with

Quellsprache: Englisch

esl-compstruct

Use when comparing two Stockholm format files with secondary structure markup to evaluate how well a test structure matches a trusted reference.

Quellsprache: Englisch

esl-construct

Use when inspecting, comparing, or rebuilding consensus RNA/DNA secondary-structure annotation in Stockholm alignments.

Quellsprache: Englisch

esl-histplot

Use when turning one numeric value per line into Easel or xmgrace histogram or survival-plot data for score-distribution analysis.

Quellsprache: Englisch

esl-mask

Use when applying coordinate-based masks to named sequences in FASTA or other Easel-supported sequence files.

Quellsprache: Englisch

esl-mixdchlet

Use when fitting, scoring, generating, or sampling mixture Dirichlet priors for count-vector data used in HMMER or Infernal-style models.

Quellsprache: Englisch

esl-reformat

Use when you need to convert sequence files between different formats such as FASTA, Stockholm, A2M, Clustal, or Phylip.

Quellsprache: Englisch

esl-selectn

Use when reservoir-sampling a fixed number of random lines from a large text file or stream without loading the whole file.

Quellsprache: Englisch

esl-seqrange

Use when splitting an SSI-indexed sequence file into per-process sequence-index ranges for embarrassingly parallel Easel or HMMER jobs.

Quellsprache: Englisch

esl-seqstat

Use when you need to compute and report statistics on biological sequence files (e.g., count, length distribution, composition) as part of HMMER/Easel workflows.

Quellsprache: Englisch

esl-sfetch

Use when you need to extract specific sequences by name from a sequence file, or index a sequence file for faster lookup.

Quellsprache: Englisch

esl-shuffle

Use when shuffling biological sequences, bootstrapping alignment columns, or generating de novo random RNA, DNA, or protein controls.

Quellsprache: Englisch

esl-ssdraw

Use when converting a Stockholm RNA or DNA alignment plus a PostScript structure template into colored secondary-structure diagrams.

Quellsprache: Englisch

esl-translate

Use when translating nucleotide sequences to amino acid sequences using Easel's translation utility from the HMMER suite.

Quellsprache: Englisch

esl-weight

Use when adding Stockholm sequence-weight annotations to nucleotide or protein MSAs before downstream HMMER-style modeling.

Quellsprache: Englisch

esummary

Use when fetching document summaries from NCBI Entrez databases by database name and identifier or accession

Quellsprache: Englisch

evo2

Use when working from the local Evo 2 repository for DNA-sequence scoring, embeddings, generation, or phage-genome design experiments.

Quellsprache: Englisch

exact-snp

Use when calling SNPs from aligned SAM/BAM reads with Subread's `exactSNP` variant caller.

Quellsprache: Englisch

exclude-uid-lists

Use when subtracting one Entrez or NCBI UID file from another and keeping only IDs unique to the first file.

Quellsprache: Englisch