Cdbfasta statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Cdbfasta

Tool usage distribution map

This map represents all the scientific publications referring to Cdbfasta per scientific context
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Cdbfasta specifications


Unique identifier OMICS_19793
Name Cdbfasta
Alternative name Fasta file indexing and retrival tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA, FA
Output format FAI
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes




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Cdbfasta citations


Genetic variation in bitter taste receptor genes influences the foraging behavior of plateau zokor (Eospalax baileyi)

Ecol Evol
PMCID: 4834321
PMID: 27110349
DOI: 10.1002/ece3.2041

[…] able S1) to conduct TBlastN searches (e‐value cutoff = 1e‐10) against the zokor genome (over 100X of sequencing depth, unpublished). For each Tas2r gene, the best‐hit scaffold was extracted using the cdbfasta program (Lee et al. ) was then aligned with the corresponding mouse gene. The primers for amplification were designed according to the flanking sequence of the zokor scaffold using Primer Pre […]


Large scale transcriptional profiling of lignified tissues in Tectona grandis

BMC Plant Biol
PMCID: 4570228
PMID: 26369560
DOI: 10.1186/s12870-015-0599-x

[…] rwise comparisons using both replicates for branch and stem secondary xylem and a cutoff of false discovery rate (FDR) < =0.05. Subsequently, differentially expressed unigenes were exported with the “cdbfasta” tool ( with the contig name from assemblies of Trinity database in .fasta format. The differentially expressed unigenes were annotated using Blast2Go []. The […]


Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample

Mol Biol Evol
PMCID: 4540967
PMID: 25957318
DOI: 10.1093/molbev/msv111

[…] im low-quality bases and remove short sequences (minimum length 150 bp; trim 3′ bases below Q20; minimum mean quality Q25; no Ns). Pairs where both reads passed quality control were extracted using a cdbfasta pipeline (script 2, Supplementary Material online) and converted to FASTA. Assemblies with IDBA-UD used a similarity threshold of 98% and minimum and maximum k values of 80 and 230 bp, respec […]


Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)

BMC Genomics
PMCID: 3898070
PMID: 24438217
DOI: 10.1186/1471-2164-15-32

[…] am [] to generate multiple-species orthologs. The orthologs not covering all the four species were discarded in further analyses. The corresponding cDNA sequences of these orthologs were extracted by cdbfasta program [] with the sequence names and were written into a single fasta file for each orthologous gene. Each fasta file contains four orthologs of a target gene. The sequences were aligned us […]

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