<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38664?offset=140 https://bioinformaticsonline.com/opportunity/view/43256/senior-scientist-bioinformatics-eurofins-genomics-india-pvt-ltd-bengaluru Sat, 14 Aug 2021 13:17:36 -0500 <![CDATA[Senior Scientist bioinformatics @ Eurofins Genomics India Pvt Ltd, Bengaluru.]]> Eurofins hiring @ Eurofins Genomics India Pvt Ltd, Bengaluru.

Designation: Senior Scientist bioinformatics
Experience: 8-9 years of experience in bioinformatics analysis of various NGS applications such as WGS, RNASeq, Metagenome, small RNA.

Location: Bangalore

Roles & Responsibilities:
-Develop NGS pipeline for analysis and interpretation of NGS data
-Organizing and managing large scale genomic data
-Should have experience in NGS data analysis, such as WGS, RNASeq, Small RNA, Metagenome (16S, ITS, Whole metagenome)etc.
-Should also have good programming skills in perl or python, PHP,J Query, MySql.
-Manage project timelines and deliverables.
-Implement and execute data processing workflows and automate the pipelines.

If you are interested, please send your profile to me at arpitaghosh@eurofins.com with “Senior Scientist bioinformatics for Genomics” as the subject.

]]> https://bioinformaticsonline.com/researchlabs/view/44666/chirag-lab-at-iisc Wed, 18 Sep 2024 01:44:37 -0500 <![CDATA[Chirag Lab at IISc]]> My research lab develops efficient computational algorithms for data-intensive problems in biology. In response to challenging computational problems, we design solutions that are provably-good, scalable in practice, and useful for life scientists to draw new insights from high-throughput data.

Research Interests
• Bioinformatics / computational biology
• Algorithms for genome sequencing
• Applied graph / combinatorial / discrete algorithms
• Algorithms design and analysis
• High performance computing

More at https://at-cg.github.io/

]]> https://bioinformaticsonline.com/bookmarks/view/33003/surankco-supervised-ranking-of-contigs-in-de-novo-assemblies Wed, 24 May 2017 04:46:52 -0500 https://bioinformaticsonline.com/bookmarks/view/33003/surankco-supervised-ranking-of-contigs-in-de-novo-assemblies <![CDATA[SuRankCo: supervised ranking of contigs in de novo assemblies]]> SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0644-7

 

Address of the bookmark: https://sourceforge.net/projects/surankco/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/2839/look-up-a-biological-numbers Fri, 23 Aug 2013 03:27:45 -0500 https://bioinformaticsonline.com/bookmarks/view/2839/look-up-a-biological-numbers <![CDATA[Look up a biological numbers]]> Did you ever need to look up a number like the volume of a cell or the cellular concentration of ATP, only to find yourself spending much more time than you wanted on the Internet or flipping through textbooks - all without much success? 

Well, it didn’t happen only to you. It is often surprising how difficult it can be to find concrete biological numbers, even for properties that have been measured numerous times. To help solve this for one and all, BioNumbers (the database of key numbers in molecular biology) was created. Along with the numbers, you'll find the relevant references to the original literature, useful comments, and related numbers. 

To cite BioNumbers please refer to: Milo et al. Nucl. Acids Res. (2010) 38: D750-D753. When using a specific entry from the database it is highly recommended that you also specify the BioNumbers 6 digit ID, e.g. "BNID 100986, Milo et al 2010". 

Address of the bookmark: http://bionumbers.hms.harvard.edu/

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/27691/histonedb-20-%E2%80%93-with-variants Fri, 03 Jun 2016 05:06:20 -0500 https://bioinformaticsonline.com/bookmarks/view/27691/histonedb-20-%E2%80%93-with-variants <![CDATA[HistoneDB 2.0 – with variants]]> This histone database can be used to explore the diversity of histone proteins and their sequence variants in many organisms. The resource was established to better understand how sequence variation may affect functional and structural features of nucleosomes. To get started, select a histone type to explore its variants.

More at http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/33976/goldgenomes-online-database Wed, 26 Jul 2017 07:49:29 -0500 https://bioinformaticsonline.com/bookmarks/view/33976/goldgenomes-online-database <![CDATA[GOLD:Genomes Online Database]]> GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43714/hiv-genome-database Fri, 21 Jan 2022 05:40:15 -0600 https://bioinformaticsonline.com/bookmarks/view/43714/hiv-genome-database <![CDATA[HIV genome database !]]> HIV resources

https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

Address of the bookmark: https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4209/enzyme-portal Tue, 03 Sep 2013 18:06:06 -0500 https://bioinformaticsonline.com/bookmarks/view/4209/enzyme-portal <![CDATA[Enzyme Portal]]> Enzyme Portal- To look for information about the biology of a protein with enzymatic activity.

The enzyme portal integrates many resources, most of them hosted by EBI and also external ones such as BioPortal. Its main goal is to provide information about enzymes in a suitable format, with a usable interface designed for intended users. Instead of reinventing the wheel, it makes use of available and reliable resources to that end.

Related Literature:

http://nar.oxfordjournals.org/content/41/D1/D773.full

http://www.biomedcentral.com/1471-2105/14/103

Address of the bookmark: http://www.ebi.ac.uk/enzymeportal/

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/39281/humcfs-a-database-of-fragile-sites-in-human-chromosomes Sun, 21 Apr 2019 20:17:29 -0500 https://bioinformaticsonline.com/bookmarks/view/39281/humcfs-a-database-of-fragile-sites-in-human-chromosomes <![CDATA[HumCFS: a database of fragile sites in human chromosomes]]> Fragile sites are specific chromosomal region that exhibit an increased frequency of chromosdomal breakge when cells are exposed to replicative stress. Since from the discovery of chromosomal fragile sites/regions (CFS), several line of evidence suggests their involvement in human pathologies and they have been recognized as a preferential site for integration of exogenous oncogenic DNA viruses and hotspots for chromosomal re-arrangement. There is large gap in our knowledge of human CFS region as knowledge about CFS are unequally distributed in literature, which impose a problem in studying these region. In order to address these issues, we develop this platform HumCFS, which provides comprehensive information about experimentally identified CFS at a single source.

https://link.springer.com/epdf/10.1186/s12864-018-5330-5?author_access_token=ICASEpyMAQaxLlKw--fyCG_BpE1tBhCbnbw3BuzI2RMA57KLmXk5bZabRUiDQzRFHXd6hjm4kWSiLV3mU5XVMitqXUwFMSo4x5vbfty0EDQ9PW1sd1h923_TYXkvJ5niSwAyZ7BklJ0ujFAFhcKtjw%3D%3D

Address of the bookmark: https://webs.iiitd.edu.in/raghava/humcfs/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/42621/busco-datasets Wed, 13 Jan 2021 19:44:33 -0600 https://bioinformaticsonline.com/bookmarks/view/42621/busco-datasets <![CDATA[BUSCO datasets !]]> 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/

]]> Jit