Tag: Comparative Genomics Resource (CGR)

New & Improved NCBI Datasets Genome and Assembly Pages

Legacy pages will be redirected effective June 2023

In June 2023, NCBI’s Assembly and Genome record pages will be redirected to new Datasets pages as part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.

We will update the following pages:

The NCBI Assembly pages will be redirected to the new Datasets Genome pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST.
The NCBI Genome pages will be redirected to the Datasets Taxonomy pages that provide a taxonomy-focused portal to genes, genomes and additional NCBI resources. 
During this transition, you will have the option to return to the legacy Genome and Assembly pages.

Continue reading “New & Improved NCBI Datasets Genome and Assembly Pages” →

Now Available! More Mammalian Cross-Species Alignments in the Comparative Genome Viewer (CGV)

In response to your feedback, we’ve made more whole genome cross-species alignments available in NCBI’s Comparative Genome Viewer (CGV). You can use these alignments to explore genome rearrangements between species. You can also zoom in to analyze regions of conserved gene synteny.

There are over 20 new cross-species alignments available, including human-mouse, mouse-rat, human-chimp, human-cattle, dog-cat, and others! These cross-species alignments provide additional opportunities to explore evolutionary relationships at the genomic and gene levels. We will add more cross-species alignments in the coming months.

The latest cross-species alignments added to CGV include imports from the UCSC Genomics Institute, as well as those generated at NCBI.

Check out two examples of cross-species whole-genome alignments in CGV below (Figure 1).

Figure 1. Whole genome alignments between (A) mouse and human (GRCm39 vs. GRCh38.p14) and (B) cat and dog (F.catus_Fca126_mat1.0 vs. ROS_Cfam_1.0). Colored bands connects aligned regions; green indicates same orientation, blue indicates opposite orientation.

When you zoom in on an alignment (Figure 2), you can compare gene annotation on the two assemblies and see the extent of conservation of synteny. You can also see which genes are missing from one or the other assembly, indicating changes in sequence or differences in annotation.

Continue reading “Now Available! More Mammalian Cross-Species Alignments in the Comparative Genome Viewer (CGV)” →

New annotations in RefSeq!

In December and January, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-nine new annotations in RefSeq for the following organisms:

Acinonyx jubatus (cheetah)
Anopheles cruzii (mosquito)
Anopheles moucheti (mosquito)
Bicyclus anynana (squinting bush brown)
Budorcas taxicolor (takin)
Carassius gibelio (silver crucian carp)
Citrus sinensis (sweet orange)
Crassostrea angulata (Portugese oyster)
Culex pipiens pallens (northern house mosquito)
Drosophila gunungcola (fruit fly)
Galleria mellonella (greater wax moth)
Gossypium arboreum (tree cotton)
Gossypium raimondii (Peruvian cotton)
Harpia harpyja (harpy eagle)
Hemicordylus capensis (graceful crag lizard)
Lactuca sativa (garden lettuce)
Mercenaria mercenaria (northern quahog)
Mya arenaria (softshell)
Octopus bimaculoides (California two-spot octopus)
Oncorhynchus keta (chum salmon)
Pangasianodon hypophthalmus (striped catfish)
Panonychus citri (citrus red mite)
Panthera uncia (snow leopard) (pictured)
Peromyscus californicus insignis (California mouse)
Podarcis raffonei (Aeolian wall lizard)
Populus trichocarpa (black cottonwood)
Scomber japonicus (chub mackerel)
Tympanuchus pallidicinctus (lesser prairie-chicken)
Vigna angularis (adzuki bean)

Continue reading “New annotations in RefSeq!” →

Announcing New Names for Eukaryotic Genome Annotations in RefSeq!

The RefSeq eukaryotic genome annotation pipeline (EGAP) is moving to a new annotation naming format that can be used to unambiguously reference both the genome assembly and the RefSeq annotation. This will improve clarity when reporting the data you use and make the data more FAIR (Findable, Accessible, Interoperable, and Reusable). The new naming convention applies to all eukaryotic annotations released after December 15, 2022.

Historically, RefSeq EGAP has used an integer to identify a particular annotation release, such as Homo sapiens Annotation Release 110. This method provides no information on the assembly used for the annotation. In the new RefSeq naming system, annotation releases are designated by a combination of the assembly identifier (e.g., GCF_000001405.40) and an annotation name (e.g., RS_2022_04). The annotation name consists of an RS prefix to indicate RefSeq annotation, and the year and month that it was generated, RS_YYYY_MM. You should always use the annotation name in combination with the corresponding assembly accession.version, for example, GCF_026419915.1-RS_2022_12 (as shown in Figure 1). This ensures that you’re always using the name that defines a specific annotation for a specific genome assembly. If you use only part of the name, it will be ambiguous.

Figure 1. The annotation section of the Datasets Genome page for the assembly bHarHar1 for the harpy eagle (Harpia harpyja) showing the new annotation release GCF_026419915.1-RS_2022_12. Continue reading “Announcing New Names for Eukaryotic Genome Annotations in RefSeq!” →

Now Available! Add your favorite organism(s) to your BLAST ClusteredNR searches

Do you currently add an organism name(s) to focus your searches when using the BLAST standard nr database? You can now focus your searches by organism with the BLAST ClusteredNR database and get faster results with a better overview of protein homologs in a wider range of organisms. Your searches will be restricted to protein clusters that contain one or more sequences from the organism(s) you add.

ClusteredNR results

A search of the ClusteredNR database (results) using human myoglobin (NP_005359.1) as a query and limited to Cetacea (whales & dolphins) returns clusters containing all the whale myoglobin matches present in a search of standard nr, as well as matches to clusters containing cytoglobin (Figure 1 A). These significant cytoglobin matches are not shown in the standard nr results with the Cetacea limit, which are dominated by matches to proteins from a single species, Physeter catodon (sperm whale) (Figure 1 B). Continue reading “Now Available! Add your favorite organism(s) to your BLAST ClusteredNR searches” →

RefSeq Release 216

RefSeq release 216 is now available online, from the FTP site, and through NCBI’s new resource, Datasets.

This full release incorporates genomic, transcript, and protein data available as of January 9, 2023, and contains 342,395,932 records, including 249,868,639 proteins, 49,869,497 RNAs, and sequences from 128,299 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq Release 216” →

New feature in the Comparative Genome Viewer!

Easily distinguish reverse orientation alignments

We are excited to announce an update to NCBI’s Comparative Genome Viewer (CGV) that allows you to quickly determine the relative orientation of aligned segments. CGV displays whole genome alignments between two different eukaryotic assemblies (Figure 1).

In the viewer, individual alignment regions are connected by colored bands between two chromosomes. These alignments are now colored differently depending on whether the aligned sequences on the two assemblies are in the same orientation (forward) or reverse orientation relative to one another. Forward orientation alignments are connected by green bands, whereas reverse alignments are connected by purple bands. Reverse alignments represent local genome inversions or inverted translocations and may point to areas of significant biological difference between the two assemblies.  Continue reading “New feature in the Comparative Genome Viewer!” →

NIH Comparative Genomics Resource project

The potential impact of emerging model organisms on human health

Comparative genomics is a science that compares genomic data either within a species or across species to answer questions in biomedicine. Laboratory experiments can then investigate the functional impact of those genomics similarities and differences. The history of comparative genomics goes back to the mid-1990s, but comparative genomics is now accelerating. A flood of new data is emerging as DNA sequencing technology becomes cheaper and commoditized. While this growth poses many challenges to current tools and approaches, it also offers immense opportunity for scientific research and understanding. These insights continue to reveal novel model organisms that can further the impact of comparative genomics on human health. Continue reading “NIH Comparative Genomics Resource project” →

Now Available! BLAST ClusteredNR database for blastx and PSI-BLAST searches

ClusteredNR, the new protein database that provides results with a better overview of protein homologs in a wider range of organisms, is now available for blastx (translated nucleotide query) and PSI-BLAST (Position Specific Iterative BLAST) searches (Figure 1). Simply select ClusteredNR in the database section of the BLAST form. You can even search standard nr at the same time to compare results.

Figure 1. Composite image from the BLAST search forms. The ClusteredNR database is available now for blastx and PSI-BLAST searches in addition to blastp. For all types of searches, you can choose to search both ClusteredNR and standard nr at the same time so you can compare results

ClusteredNR is especially useful with blastx for finding more distant homologs when searching with queries from over-represented groups. For PSI-BLAST, the greater taxonomic scope of ClusteredNR database allows you to work more effectively with the default number target sequences in the first round. The two searches described below highlight these advantages of ClusteredNR.

Continue reading “Now Available! BLAST ClusteredNR database for blastx and PSI-BLAST searches” →

New RefSeq Annotations!

In October and November, the NCBI Eukaryotic Genome Annotation Pipeline released thirty-one new annotations in RefSeq for the following organisms:

Acanthochromis polyacanthus (spiny chromis)
Acomys russatus (golden spiny mouse)
Andrographis paniculata (eudicot)
Antechinus flavipes (yellow-footed antechinus)
Apodemus sylvaticus (European woodmouse)
Apus apus (common swift)
Arachis duranensis (eudicot)
Continue reading “New RefSeq Annotations!” →