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41 to 50 of 1,940 Results

01b_ccar_genome_v1_262scaffolds_sm_fasta.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 1.6 GB - MD5: 3055c321971811144243b5d91b3998dd Datagenome This is the soft-masked version of the genome used in some steps of the annotation pipeline (see article for details). The genome was soft-masked using Repeatmodeler.
02a_ccar_genome_v1_262scaffolds_trna_gff3.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 2.6 MB - MD5: e1ff55cd7f6075ef495e208664c34d5c This file contains the transfer RNAs (tRNAs) predicted by the tool tRNAScan-SE.
02b_ccar_genome_v1_262scaffolds_rrna_gff3.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 1.6 MB - MD5: 47ca43fd1ed2cf989f2bbfa340f19723 This file contains annotations of ribosomal RNAs predicted by RNAammer.
02c_ccar_isoseq_hq_transcripts_fasta.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 646.7 MB - MD5: ffedfa19d89406f2305beae31e83a54b
02d_ccar_annotation_v5_gff3.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 212.8 MB - MD5: 54423b6fc680239a4171338b33a6f4f1
03a_ccar_annotation_v5_proteins_fasta.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 55.7 MB - MD5: 2685ca29c2c6ab6e4843b20eec9ffe59 This is the predicted amino acid sequences from the genome (262 scaffolds) in fasta format. The sequences were extracted using the AGAT script "agat_sp_extract_sequences.pl" in Anaconda3 (2022.10 on Saga).
03b_ccar_annotation_v5_transcripts_fasta.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 228.7 MB - MD5: e3981b08eeb941b6770b6d8e592b8612 This is the predicted transcript sequences from the genome (262 scaffolds) in fasta format. The sequences were extracted using the AGAT script "agat_sp_extract_sequences.pl" in Anaconda3 (2022.10 on Saga).
04a_ccar_annotation_v5_kegg.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 5.3 MB - MD5: c544d1acf5320b0b9a4180c91e07d31f This file contains the output of the search for KEGG ortholog (KO) matches in the KEGG Ortholog database, found using the tool BlastKOALA (v. 3; https://www.kegg.jp/blastkoala/).
04b_ccar_annotation_v5_interproscan.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 245.2 MB - MD5: 44c621da5dce702d556d1324ce651cfc This is the output from the search run using InterProScan (5.62-94.0-foss-2022a on Saga) against the following databases (version): FunFam (4.3.0), SFLD (4), PANTHER (17.0), Gene3D (4.3.0), Hamap (2023_01), PRINTS (42.0), ProSiteProfiles (2022_05), Coils (2.2.1), SUPERFAMILY (1.7...
05_ccar_genome_v1_scaffold_107_mito_NCBI.txt Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Plain Text - 3.2 KB - MD5: ede1f0b01f51653c8723e8656e6aaa5c This file contain the mitochondrial genome annotation in NCBI format. The annotation was made using the tool MitoAnnotator (

01b_ccar_genome_v1_262scaffolds_sm_fasta.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 1.6 GB -

Datagenome

This is the soft-masked version of the genome used in some steps of the annotation pipeline (see article for details). The genome was soft-masked using Repeatmodeler.

02a_ccar_genome_v1_262scaffolds_trna_gff3.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 2.6 MB -

This file contains the transfer RNAs (tRNAs) predicted by the tool tRNAScan-SE.

02b_ccar_genome_v1_262scaffolds_rrna_gff3.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 1.6 MB -

This file contains annotations of ribosomal RNAs predicted by RNAammer.

02c_ccar_isoseq_hq_transcripts_fasta.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 646.7 MB -

02d_ccar_annotation_v5_gff3.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 212.8 MB -

03a_ccar_annotation_v5_proteins_fasta.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 55.7 MB -

This is the predicted amino acid sequences from the genome (262 scaffolds) in fasta format. The sequences were extracted using the AGAT script "agat_sp_extract_sequences.pl" in Anaconda3 (2022.10 on Saga).

03b_ccar_annotation_v5_transcripts_fasta.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 228.7 MB -

This is the predicted transcript sequences from the genome (262 scaffolds) in fasta format. The sequences were extracted using the AGAT script "agat_sp_extract_sequences.pl" in Anaconda3 (2022.10 on Saga).

04a_ccar_annotation_v5_kegg.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 5.3 MB -

This file contains the output of the search for KEGG ortholog (KO) matches in the KEGG Ortholog database, found using the tool BlastKOALA (v. 3; https://www.kegg.jp/blastkoala/).

04b_ccar_annotation_v5_interproscan.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 245.2 MB -

This is the output from the search run using InterProScan (5.62-94.0-foss-2022a on Saga) against the following databases (version): FunFam (4.3.0), SFLD (4), PANTHER (17.0), Gene3D (4.3.0), Hamap (2023_01), PRINTS (42.0), ProSiteProfiles (2022_05), Coils (2.2.1), SUPERFAMILY (1.7...

05_ccar_genome_v1_scaffold_107_mito_NCBI.txt

Feb 10, 2025 - Replication Data for: Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

Plain Text - 3.2 KB -

This file contain the mitochondrial genome annotation in NCBI format. The annotation was made using the tool MitoAnnotator (

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