Microbial ecology
ENV-412
NCBI-BLAST
Description
National Center for Biotechnology Information (NCBI) contains multiple publicly available databases, including genomic sequences. NCBI also has the BLAST tool.
Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. BLAST can take sequences of nucleotides or proteins and search them agains the entire publicly available database. Try taking some of your nucleotide sequences (from your genomes) to BLAST them.
Each of your genomes comes in a ".fa" file. This is a type of FASTA file. FASTA format is a text-based file for nucleotide (genomic) or animo acid (protein) sequences. You have nucleotide sequences. A FASTA file can have multiple sequences in it.
A sequence in a FASTA file begins with a greater-than character (">") followed by a description of the sequence (all in a single line). This is called the FASTA header. The lines immediately following the description line is the nucleotide (or amino acid) sequence.
Each of your genome .fa files contains multiple sequences that we were able to generate with the sequencing.
Each sequence will look something like this:
>tig00000036
CCGCTGACCCATCTGGTGAGTTCCTGGAGCCTGGAGCAGGCC
GTCGAGCGCCTTCAGGTTCTCGGCGACGGCGCCGGGCCGTT
GGGTGGGCGAGGAAGTCGTCGTACGCGTAGGGGAAGTCC
In your cases the FASTA header is not very informative, but this is normal for output from sequencing.
Try the BLAST tool on NCBI with your sequences. Make sure to use "nucleotide > nucleotide" (also known as blastn) as you are searching your nucleotide sequences agains the entire nucleotide sequence database. The tool starts off with default values, you can keep these (you have to hit the BLAST button at the bottom, after copy/pasting your sequence. Do only one sequence at a time (remember the sequences in the FASTA file are separated by a ">" sign. You don't need to BLAST all of your sequences (there are too many), but check a few to give yourself an idea what organism you have. Explore the output.
https://blast.ncbi.nlm.nih.gov/Blast.cgi
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome