BOL: Related items

Updated ranking of institutes and countries based on developed biological databases

Rahul Nayak — Fri, 11 Jan 2019 09:35:26 -0600

Updated ranking of institutes and countries based on developed biological databases is available at https://lnkd.in/fiVAdM6 , India is maintaing 4th position and "Institute of Microbial Technology, Chandigarh" is on 3rd Position (after EBI and NCBI). This is a big achievement for any institute to reach on 3rd position in the world.

More at http://bigd.big.ac.cn/databasecommons/stat

BUSCO datasets !

Jit — Wed, 13 Jan 2021 19:44:33 -0600

The BUSCO software now directly downloads the necessary datasets, specified by the user or automatically selected.

To display all available datasets

busco --list-datasets

You can also download them manually and see a list with the number of marker genes.

Earlier versions: v3, v2, v1

../
acidobacteria_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     14M
aconoidasida_odb10.2020-08-05.tar.gz               16-Oct-2020 13:19     51M
actinobacteria_class_odb10.2020-03-06.tar.gz       16-Oct-2020 13:19      8M
actinobacteria_phylum_odb10.2020-03-06.tar.gz      16-Oct-2020 13:20      9M
actinopterygii_odb10.2020-08-05.tar.gz             16-Oct-2020 13:20    173M
agaricales_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:20    186M
agaricomycetes_odb10.2020-08-05.tar.gz             16-Oct-2020 13:19    152M
alphaproteobacteria_odb10.2020-03-06.tar.gz        16-Oct-2020 13:20     11M
alteromonadales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:20     18M
alveolata_odb10.2020-09-10.tar.gz                  16-Oct-2020 13:20     13M
apicomplexa_odb10.2020-09-10.tar.gz                16-Oct-2020 13:19     27M
aquificae_odb10.2020-03-06.tar.gz                  16-Oct-2020 13:19     12M
arachnida_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    136M
archaea_odb10.2020-03-06.tar.gz                    16-Oct-2020 13:20      4M
arthropoda_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:20     95M
ascomycota_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:20    295M
aves_odb10.2020-09-10.tar.gz                       16-Oct-2020 13:20    465M
bacillales_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20     10M
bacilli_odb10.2020-03-06.tar.gz                    16-Oct-2020 13:19      7M
bacteria_odb10.2020-03-06.tar.gz                   16-Oct-2020 13:20      6M
bacteroidales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:20     13M
bacteroidetes-chlorobi_group_odb10.2020-03-06.t..> 16-Oct-2020 13:19      9M
bacteroidetes_odb10.2020-03-06.tar.gz              16-Oct-2020 13:20     10M
bacteroidia_odb10.2020-03-06.tar.gz                16-Oct-2020 13:20     13M
basidiomycota_odb10.2020-09-10.tar.gz              16-Oct-2020 13:19    165M
betaproteobacteria_odb10.2020-03-06.tar.gz         16-Oct-2020 13:19     13M
boletales_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    197M
brassicales_odb10.2020-08-05.tar.gz                16-Oct-2020 13:20    158M
burkholderiales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     16M
campylobacterales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:20     14M
capnodiales_odb10.2020-08-05.tar.gz                16-Oct-2020 13:19    178M
carnivora_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    376M
cellvibrionales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     19M
cetartiodactyla_odb10.2020-08-05.tar.gz            16-Oct-2020 13:19    407M
chaetothyriales_odb10.2020-08-05.tar.gz            16-Oct-2020 13:20    288M
chlamydiae_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20     13M
chlorobi_odb10.2020-03-06.tar.gz                   16-Oct-2020 13:20     22M
chloroflexi_odb10.2020-03-06.tar.gz                16-Oct-2020 13:20      6M
chlorophyta_odb10.2020-08-05.tar.gz                16-Oct-2020 13:20     58M
chromatiales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     14M
chroococcales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     27M
clostridia_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:19      6M
clostridiales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:20      6M
coccidia_odb10.2020-08-05.tar.gz                   16-Oct-2020 13:20     24M
coriobacteriales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     12M
coriobacteriia_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20      9M
corynebacteriales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:19     16M
cyanobacteria_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     17M
cyprinodontiformes_odb10.2020-08-05.tar.gz         16-Oct-2020 13:19    504M
cytophagales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     18M
cytophagia_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20     18M
delta-epsilon-subdivisions_odb10.2020-03-06.tar.gz 16-Oct-2020 13:19      6M
deltaproteobacteria_odb10.2020-03-06.tar.gz        16-Oct-2020 13:19      6M
desulfobacterales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:20     13M
desulfovibrionales_odb10.2020-03-06.tar.gz         16-Oct-2020 13:19     17M
desulfurococcales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:20      9M
desulfuromonadales_odb10.2020-03-06.tar.gz         16-Oct-2020 13:19     18M
diptera_odb10.2020-08-05.tar.gz                    16-Oct-2020 13:19    185M
dothideomycetes_odb10.2020-08-05.tar.gz            16-Oct-2020 13:19    194M
embryophyta_odb10.2020-09-10.tar.gz                16-Oct-2020 13:19    138M
endopterygota_odb10.2020-09-10.tar.gz              16-Oct-2020 13:19    190M
enterobacterales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     11M
entomoplasmatales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:19      7M
epsilonproteobacteria_odb10.2020-03-06.tar.gz      16-Oct-2020 13:20     13M
euarchontoglires_odb10.2020-09-10.tar.gz           16-Oct-2020 13:20    728M
eudicots_odb10.2020-09-10.tar.gz                   16-Oct-2020 13:19    168M
euglenozoa_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:20     10M
eukaryota_odb10.2020-09-10.tar.gz                  16-Oct-2020 13:19    100M
eurotiales_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:19    211M
eurotiomycetes_odb10.2020-08-05.tar.gz             16-Oct-2020 13:19    197M
euryarchaeota_odb10.2020-03-06.tar.gz              16-Oct-2020 13:20      5M
eutheria_odb10.2020-09-10.tar.gz                   16-Oct-2020 13:20    920M
fabales_odb10.2020-08-05.tar.gz                    16-Oct-2020 13:19    184M
firmicutes_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20      6M
flavobacteriales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     18M
flavobacteriia_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20     18M
fungi_odb10.2020-09-10.tar.gz                      16-Oct-2020 13:19    181M
fusobacteria_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     11M
fusobacteriales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     11M
gammaproteobacteria_odb10.2020-03-06.tar.gz        16-Oct-2020 13:19     10M
glires_odb10.2020-08-05.tar.gz                     16-Oct-2020 13:19    549M
glomerellales_odb10.2020-08-05.tar.gz              16-Oct-2020 13:19    259M
halobacteria_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     18M
halobacteriales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:20     18M
haloferacales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     20M
helotiales_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:19    224M
hemiptera_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    115M
hymenoptera_odb10.2020-08-05.tar.gz                16-Oct-2020 13:19    321M
hypocreales_odb10.2020-08-05.tar.gz                16-Oct-2020 13:19    224M
insecta_odb10.2020-09-10.tar.gz                    16-Oct-2020 13:20    119M
lactobacillales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19      9M
laurasiatheria_odb10.2020-09-10.tar.gz             16-Oct-2020 13:20    688M
legionellales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     16M
leotiomycetes_odb10.2020-08-05.tar.gz              16-Oct-2020 13:19    164M
lepidoptera_odb10.2020-08-05.tar.gz                16-Oct-2020 13:20    241M
liliopsida_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:20    163M
mammalia_odb10.2020-09-10.tar.gz                   16-Oct-2020 13:19    677M
metazoa_odb10.2020-09-10.tar.gz                    16-Oct-2020 13:19    127M
methanobacteria_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     15M
methanococcales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:20     17M
methanomicrobia_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     12M
methanomicrobiales_odb10.2020-03-06.tar.gz         16-Oct-2020 13:20     16M
micrococcales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     12M
microsporidia_odb10.2020-08-05.tar.gz              16-Oct-2020 13:20     26M
mollicutes_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:20      3M
mollusca_odb10.2020-08-05.tar.gz                   16-Oct-2020 13:20    266M
mucorales_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:20    105M
mucoromycota_odb10.2020-08-05.tar.gz               16-Oct-2020 13:19     75M
mycoplasmatales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19      4M
natrialbales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     24M
neisseriales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     16M
nematoda_odb10.2020-08-05.tar.gz                   16-Oct-2020 13:20    138M
nitrosomonadales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     15M
nostocales_odb10.2020-03-06.tar.gz                 16-Oct-2020 13:19     35M
oceanospirillales_odb10.2020-03-06.tar.gz          16-Oct-2020 13:19     13M
onygenales_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:19    233M
oscillatoriales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     29M
passeriformes_odb10.2020-08-05.tar.gz              16-Oct-2020 13:20    298M
pasteurellales_odb10.2020-03-06.tar.gz             16-Oct-2020 13:19     19M
planctomycetes_odb10.2020-03-06.tar.gz             16-Oct-2020 13:19     13M
plasmodium_odb10.2020-08-05.tar.gz                 16-Oct-2020 13:20    199M
pleosporales_odb10.2020-08-05.tar.gz               16-Oct-2020 13:19    288M
poales_odb10.2020-08-05.tar.gz                     16-Oct-2020 13:19    186M
polyporales_odb10.2020-08-05.tar.gz                16-Oct-2020 13:20    206M
primates_odb10.2020-08-05.tar.gz                   16-Oct-2020 13:19    451M
propionibacteriales_odb10.2020-03-06.tar.gz        16-Oct-2020 13:19     14M
proteobacteria_odb10.2020-03-06.tar.gz             16-Oct-2020 13:19      8M
pseudomonadales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     17M
rhizobiales_odb10.2020-03-06.tar.gz                16-Oct-2020 13:19     15M
rhizobium-agrobacterium_group_odb10.2020-03-06...> 16-Oct-2020 13:19     34M
rhodobacterales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     19M
rhodospirillales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     14M
rickettsiales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19      8M
saccharomycetes_odb10.2020-08-05.tar.gz            16-Oct-2020 13:20    109M
sauropsida_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:19    499M
selenomonadales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     16M
solanales_odb10.2020-08-05.tar.gz                  16-Oct-2020 13:19    196M
sordariomycetes_odb10.2020-08-05.tar.gz            16-Oct-2020 13:19    206M
sphingobacteriia_odb10.2020-03-06.tar.gz           16-Oct-2020 13:20     21M
sphingomonadales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:19     22M
spirochaetales_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20      8M
spirochaetes_odb10.2020-03-06.tar.gz               16-Oct-2020 13:20      6M
spirochaetia_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19      6M
stramenopiles_odb10.2020-08-05.tar.gz              16-Oct-2020 13:19      5M
streptomycetales_odb10.2020-03-06.tar.gz           16-Oct-2020 13:20     31M
streptosporangiales_odb10.2020-03-06.tar.gz        16-Oct-2020 13:19     22M
sulfolobales_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19     22M
synechococcales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     16M
synergistetes_odb10.2020-03-06.tar.gz              16-Oct-2020 13:19     14M
tenericutes_odb10.2020-03-06.tar.gz                16-Oct-2020 13:20      4M
tetrapoda_odb10.2020-09-10.tar.gz                  16-Oct-2020 13:19    561M
thaumarchaeota_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20     13M
thermoanaerobacterales_odb10.2020-03-06.tar.gz     16-Oct-2020 13:19     10M
thermoplasmata_odb10.2020-03-06.tar.gz             16-Oct-2020 13:20      7M
thermoproteales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19      8M
thermoprotei_odb10.2020-03-06.tar.gz               16-Oct-2020 13:20      6M
thermotogae_odb10.2020-03-06.tar.gz                16-Oct-2020 13:19     16M
thiotrichales_odb10.2020-03-06.tar.gz              16-Oct-2020 13:20     11M
tissierellales_odb10.2020-03-06.tar.gz             16-Oct-2020 13:19      9M
tissierellia_odb10.2020-03-06.tar.gz               16-Oct-2020 13:19      8M
tremellomycetes_odb10.2020-08-05.tar.gz            16-Oct-2020 13:19    210M
verrucomicrobia_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     11M
vertebrata_odb10.2020-09-10.tar.gz                 16-Oct-2020 13:19    409M
vibrionales_odb10.2020-03-06.tar.gz                16-Oct-2020 13:20     26M
viridiplantae_odb10.2020-09-10.tar.gz              16-Oct-2020 13:20     36M
xanthomonadales_odb10.2020-03-06.tar.gz            16-Oct-2020 13:19     24M

Address of the bookmark: https://busco-data.ezlab.org/v4/data/lineages/

ncbi-datasets-cli -- Quickstart: command line tools !

Jit — Tue, 07 Dec 2021 02:51:26 -0600

Install and use the NCBI Datasets command line tools

The NCBI Datasets datasets command line tools are datasets and dataformat .

Use datasets to download biological sequence data across all domains of life from NCBI.

Use dataformat to convert metadata from JSON Lines format to other formats.

Conda download:

https://anaconda.org/conda-forge/ncbi-datasets-cli

Buld Download

https://www.ncbi.nlm.nih.gov/datasets/builder/?tax_id=29979

Address of the bookmark: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/quickstarts/command-line-tools/

dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation

Jit — Mon, 29 May 2017 05:39:29 -0500

dbCAN is a web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE. Similar resources on the web include CAZy database and CAT. All data in dbCAN are generated based on the family classification from CAZy database while it has the following unique features compared with CAZy database and CAT:

dbCAN provides the capability of automated and comprehensive CAZyme annotation of a given genome submitted by the user;
dbCAN provides an explicitly defined signature domain for each and every CAZyme family along with its location in all the relevant full-length CAZyme proteins in all sequenced genomes;
dbCAN provides the most complete set of metagenomic CAZyme genes published so far and represents the first step towards discovering novel CAZyme catalysts in metagenomes;
dbCAN provides a subfamily classification of the existing CAZyme families based on sequence similarities;
dbCAN make all pre-computed data freely available to the public, including sequence alignments, hidden markov models (HMMs) and phylogenies of the signature domain regions in each and every CAZyme family and subfamily.

dbCAN is updated regularly when CAZy database created new families based on latest literature.

Address of the bookmark: http://csbl.bmb.uga.edu/dbCAN/index.php

ENCODE3: A collection of research articles and related content describing the Encyclopedia of DNA Elements, its datasets and tools.

Shruti Paniwala — Sat, 08 Aug 2020 08:25:21 -0500

How cells, tissues and organisms interpret the information encoded in the genome has vital implications for our understanding of development, health and disease. Launched in 2003, the ENCyclopedia Of DNA Elements (ENCODE) project has the aim of mapping the functional elements in the human genome (later expanded to include model organisms).

During the first phase of ENCODE, published in 2007, microarray-based technologies were used to detect regions associated with transcription factors, certain histone modifications and open chromatin within a pre-specified 1% of the human genome.

ENCODE’s second phase saw a switch to sequencing-based technologies, the addition of new assay types and the analysis of functional elements genome-wide, described in a collection of research articles in 2012.

The Encyclopedia paper of ENCODE 3, published in Nature, gives an overview of the various assays that were performed in human and mouse cell lines and tissues and describes a Registry of human and mouse candidate cis-regulatory elements (cCREs).

More at https://www.nature.com/immersive/d42859-020-00027-2/index.html

HELIANO: A fast and accurate tool for detection of Helitron-like elements

LEGE — Tue, 13 Aug 2024 07:16:34 -0500

Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging to identify. Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae679/7730539?login=true

Address of the bookmark: https://github.com/Zhenlisme/heliano/

RepeatModeler2: automated genomic discovery of transposable element families

Neel — Mon, 02 Dec 2019 06:52:29 -0600

RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, https://github.com/Dfam-consortium/TETools).

Address of the bookmark: https://github.com/Dfam-consortium/TETools

XAMPP: Starting Apache fail Ubuntu

Ram Yash Pal — Sat, 07 Jun 2014 05:52:35 -0500

Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it.

sudo /etc/init.d/apache2 stop

sudo /etc/init.d/mysql stop

sudo /etc/init.d/proftpd stop

sudo /opt/lampp/lampp start

PhpMyAdmin “Wrong permissions on configuration file, should not be world writable!”

Once the Xammp is installed, it might be possible to set up the configuration file in writable mode. Try the following steps:

Just chmod 0755 the file

sudo chmod 0755 config.inc.php

4DGenome

Jitendra Narayan — Mon, 04 Jul 2016 00:44:55 -0500

Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted interactions in 5 organisms. Experimental data cover both high throughput datasets and individiual focused studies.

All interaction data are freely available in a standardized file format. Records can be queried by genomic regions, gene names, organism, and detection technology.

Address of the bookmark: http://4dgenome.research.chop.edu/

Reactome Pathway Database

BioStar — Mon, 31 Dec 2018 02:41:33 -0600

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome analysis, modeling, systems biology and education. Founded in 2003, the Reactome project is led by Lincoln Stein of OICR, Peter D’Eustachio of NYULMC, Henning Hermjakob of EMBL-EBI, and Guanming Wu of OHSU.

Address of the bookmark: https://reactome.org/