Cdbfasta statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Cdbfasta
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Tool usage distribution map

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

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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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  • person_outline Geo Pertea

Cdbfasta citations

 (4)
library_books

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

2016
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able S1) to conduct TBlastN searches (e‐value cutoff = 1e‐10) against the zokor genome (over 100X of sequencing depth, unpublished).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 […]

library_books

Large scale transcriptional profiling of lignified tissues in Tectona grandis

2015
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 (http://compbio.dfci.harvard.edu/) with the contig name from assemblies of Trinity database in .fasta format. The differentially expressed unigenes were annotated using Blast2Go []. The […]

library_books

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

2015
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 […]

library_books

Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)

2014
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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