BOL: Related items

Understanding DUMP files from NCBI Taxonomy database !

Shruti Paniwala — Fri, 15 Jul 2022 04:29:05 -0500

*.dmp files are bcp-like dump from GenBank taxonomy database

General information.

Field terminator is "\t|\t"

Row terminator is "\t|\n"

nodes.dmp file consists of taxonomy nodes. The description for each node includes the following

fields:

tax_id -- node id in GenBank taxonomy database

parent tax_id -- parent node id in GenBank taxonomy database

rank -- rank of this node (superkingdom, kingdom, ...)

embl code -- locus-name prefix; not unique

division id -- see division.dmp file

inherited div flag (1 or 0) -- 1 if node inherits division from parent

genetic code id -- see gencode.dmp file

inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent

mitochondrial genetic code id -- see gencode.dmp file

inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent

GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage

hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet

comments -- free-text comments and citations

Taxonomy names file (names.dmp):

tax_id -- the id of node associated with this name

name_txt -- name itself

unique name -- the unique variant of this name if name not unique

name class -- (synonym, common name, ...)

Divisions file (division.dmp):

division id -- taxonomy database division id

division cde -- GenBank division code (three characters)

division name -- e.g. BCT, PLN, VRT, MAM, PRI...

comments

Genetic codes file (gencode.dmp):

genetic code id -- GenBank genetic code id

abbreviation -- genetic code name abbreviation

name -- genetic code name

cde -- translation table for this genetic code

starts -- start codons for this genetic code

Deleted nodes file (delnodes.dmp):

tax_id -- deleted node id

Merged nodes file (merged.dmp):

old_tax_id -- id of nodes which has been merged

new_tax_id -- id of nodes which is result of merging

Citations file (citations.dmp):

cit_id -- the unique id of citation

cit_key -- citation key

pubmed_id -- unique id in PubMed database (0 if not in PubMed)

medline_id -- unique id in MedLine database (0 if not in MedLine)

url -- URL associated with citation

text -- any text (usually article name and authors).

-- The following characters are escaped in this text by a backslash:

-- newline (appear as "\n"),

-- tab character ("\t"),

-- double quotes ('\"'),

-- backslash character ("\\").

taxid_list -- list of node ids separated by a single space

Reference Sequence Resource!

LEGE — Wed, 15 Sep 2021 21:15:22 -0500

The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse (mm9/mm10) genomes for historical comparability. Drosophia melanogaster experiments are mapped to either dm3 or dm6 and Caenorhabdilis elegans experiments are mapped to ce10 or ce11. T

Address of the bookmark: https://www.encodeproject.org/data-standards/reference-sequences/

GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research

Rahul Nayak — Sat, 26 Jan 2019 18:58:16 -0600

GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).

Address of the bookmark: https://github.com/b-brankovics/grabb

SEASTAR: Systematic Evaluation of Alternative STArt site in RNA

BioStar — Thu, 13 Aug 2020 09:54:27 -0500

SEASTAR (Systematic Evaluation of Alternative STArt site in RNA) is a software package for Transcription Start Site (TSS) identification and quantification using only RNA-seq data. It assembles novel TSSs based only on RNA-Seq data and merges them with known TSSs from a public database. This package enables high-quality TSS identification that is comparable to the highly sophisticated CAGE technology. This package is particularly useful for finding novel TSSs that contribute to transcriptome complexity along with identifying differential promoter utilization.

version 1.0.0 - updates several descriptions and tests. To achieve v0.9.4, one can visit https://github.com/zhyqin/SEASTAR-0.9.4 for download.

Address of the bookmark: https://github.com/Xinglab/SEASTAR

NCBI PSI-BLAST Tutorial

Wed, 04 Sep 2013 11:46:06 -0500

http:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are related to a sequence that the user provides.

BLAST+ updated !!!

Jit — Tue, 16 Jun 2015 16:55:24 -0500

A new version (2.2.31) of the stand-alone BLAST executables (Linux, Windows and MacOSX on FTP) is now available. New features include support for BLAST-XML2 specification (information here) and JSON BLAST output format, as well as several bug fixes and improvements. The BLAST AMI at AWS will also be updated to 2.2.31 (see this BLAST Help page for more information). For a full list of improvements, see the release notes.

More at http://www.ncbi.nlm.nih.gov/news/06-16-2015-blast-plus-update/?

sequenceserver

Jit — Fri, 10 Mar 2017 08:51:55 -0600

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.

More at http://sequenceserver.com.

Address of the bookmark: https://github.com/wurmlab/sequenceserver

NCBI Magic-BLAST

Jit — Tue, 14 Aug 2018 18:11:11 -0500

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

Address of the bookmark: https://ncbi.github.io/magicblast/

Primer BLAST !

BioStar — Tue, 28 Apr 2020 00:28:49 -0500

BLAST team added a new feature (Max 3' match), shown in Figure 1, to Primer-BLAST that limits the length of 3' exon matches when designing exon-exon spanning primers. This makes it less likely that primers specifically designed to amplify transcripts will also amplify genomic DNA contamination in expression assays. See the NCBI Insights post (https://go.usa.gov/xvUT4) for more details.

If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.gov

Cleaner BLAST Databases for More Accurate Results

LEGE — Tue, 23 Apr 2024 01:23:08 -0500

Do you use BLAST to identify a sequence or the evolutionary scope of a gene? That can be challenging if contaminated and misclassified sequences are in the BLAST databases and show up in your search results. To address this problem, we now use the NCBI quality assurance tools listed below to systematically remove these misleading sequences from the default nucleotide (nt) and protein (nr) BLAST databases.

Foreign Contamination Screen tool for genome cross-species screening (FCS-GX) detects contamination from foreign organisms in genomes and other sequences using the genome cross-species aligner (GX)
Average Nucleotide Identity (ANI) evaluates the taxonomic classification of prokaryotic genome assemblies. Sequences from genomes marked up as ‘unverified source organism’ are considered suspect and removed.

Ref https://ncbiinsights.ncbi.nlm.nih.gov/2024/04/22/cleaner-blast-databases-more-accurate-results/