BOL: Results for "FASTA"

Results for "FASTA"

- Jit@jit.aber
Computer simulation of genetic mechanism !!
...tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC content across a genome to model new genomes in FASTA format while tracking applied...
2966 days ago
- Jit@jit.aber
Ancestral sequence reconstruction (ASR) or ancestral gene/sequence reconstruction/resurrection tools to study molecular evolution
...phylogenetic tree. It is designed for large-scale studies, including simulation of multiple replicates and outputs sequences into NEXUS, MEGA, or FASTA formats. MySSP has a fairly s...
2521 days ago
+7 more Blogs

- Rahul Agarwal@raag
Download mutliple fasta file from NCBI in one GO!!
...then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click giv...\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' GIs.txt >sequence.fasta where GIs.txt contains ...
3901 days ago
- Abhimanyu Singh@abhimanyu
Barrnap: Bacterial ribosomal RNA predictor
...genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and wr...
2541 days ago
+58 more Bookmarks

- Jit@jit.aber
Detect the sequence pattern and its location in fasta file with match and mismatches information.
This script is one of my old script to detect some centromeric pattern in chromosomes. User can also control the number of mismatches allowed through command line .. To run: perl centro.pl
3858 days ago
- Jit@jit.aber
Clean the FASTA file
Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.
3857 days ago
+1 more Files

- Jitendra Narayan@admin
Useful Links for Bioinformaticians
...o analysing sequence databases Sequence Comparison (Keith Robison) Database Research at Penn Biology, E. W. Myers Bill Pearson talks about Fasta Bioinformatics: Elementary S...
3121 days ago
- Abhimanyu Singh@abhimanyu
Perl one-liner for bioinformatician !!!
...otations/ http://genomics-array.blogspot.com/2010/11/some-unixperl-oneliners-for.html http://bioexpressblog.wordpress.com/2013/04/05/split-multi-fasta-sequence-file/
3619 days ago
+17 more Top-level pages

- Rahul Nayak@rahul
GenBank to FASTA format conversion, Written By Junguk HUR http://tinyurl.com/ntp7w5v #Perl #FASTA #Genbank
3859 days ago
- Jit@jit.aber
perl -nle 'if (/^>/) { $sl = 0; print; next } next if ($sl >= 200); $_ = substr($_, 0, 200-$sl) if ($sl + length($_) > 200); $sl += length($_); print;' file.fa >new.fa #Perl #Extract #Fasta
3612 days ago
+81 more Wire posts

- ArrayGen Technologies@arraygen
ArrayGen Next Generation Genome Browser Coming Soon !!!
...nalysis. It is platform independent and much simpler to use. The main features are, it supports many standard file formats such as GFF, BED, GTF, FASTA, VCF, BAM and it can be integ...
3067 days ago
- Jit@jit.aber
New Layout for BLAST ftp Database Site
...v4 subdirectory. As of 1/13/20 the Cloud directory will be frozen with no more new entries. The will be no more updates to dbV4 databases. The FASTA directory will contain nr, nt...
1556 days ago

- Robert M Willioms@robert
Sequence Viewer: Download Transcripts, Exons and Proteins
How to download FASTA sequence for certain gene features while in the NCBI's Sequence Viewer. Sequence Viewer homepage: www.ncbi.nlm.nih.gov/projects/sviewer/ Sequence Viewer playlist: https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C3
3510 days ago

- Surabhi Chaudhary@surabhi
Python script to download covid genome !
...x['gene-region'] == "complete": nm = x['accession'] print("downloading", nm) dna = Entrez.efetch(db='nucleotide',id=nm, rettype = 'fasta', retmode= 'text').read().spl...
1127 days ago
- Neelam Jha@neelam
Download genome using NCBI esearch command line !
...cleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003784.1" | efetch -format fasta > seq2.fa #fastANI for ali...fastANI -q seq1.fa -r seq2.fa --visualize -o fastani.out #Plot using sequence...
1092 days ago
+109 more Bio-Scripts

- LEGE@lege
Comment on "Short-read assembly using Spades !"
...output: Once SPAdes has finished running, check the output directory for the assembled contigs. The contigs will be saved in a file named contigs.fasta. You can view the contigs usi...
411 days ago
- BioStar@biostar
Comment on "Basic command-line to run BLAST"
...nd tblastx. Choose the program that is appropriate for your query and database. Prepare the query sequence: The query sequence should be in a FASTA format and can be entered dir...
414 days ago
+27 more Comments