User: suzuBell
suzuBell • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- Last seen:
- 14 hours ago
- Joined:
- 3 months ago
- Email:
- l****************@gmail.com
Posts by suzuBell
<prev
• 15 results •
page 1 of 2 •
next >
0
votes
2
answers
41
views
2
answers
... I have three protein .fasta files (file1.fasta, file2.fasta, and file3.fasta), each in the following format:
>MOLCJCMO_00002 [gene=cysS] [locus_tag=HCW_RS04050] [protein=cysteine--tRNA ligase] [protein_id=WP_014660951.1][location=complement(860733..862130)] [gbkey=CDS]
MKIFDTHLKQKVPFEPLI ...
written 14 hours ago by
suzuBell • 40
• updated
10 hours ago by
Mensur Dlakic • 2.4k
0
votes
1
answer
136
views
1
answer
... I have the 16S rRNA sequence of a new strain of bacteria. I would like to make a simple phylogenetic tree visualization comparing this new strain of bacteria with about 12 other strains of known bacteria. Currently, I have 13 .fastq files (one being the new strain of bacteria), each containing a 16S ...
written 29 days ago by
suzuBell • 40
• updated
29 days ago by
Mensur Dlakic • 2.4k
2
votes
0
answers
137
views
0
answers
... I have been finding the Prokka software to be very useful annotating an assembled bacterial genome (contigs). I am trying to determine whether this assembled genome contains any "mobile DNAs" (and if so, how many, and their names). Is this something that can be interpreted easily from the Prokka out ...
9
votes
3
answers
208
views
8 follow
3
answers
... I have been finding the [Prokka software][1] to be very useful annotating an assembled bacterial genome (contigs). I wanted to know if anyone has recommendations on how to determine if the assembled bacterial genome (contigs) contains a plasmid. If so, how many plasmids and length of plasmids.
I tr ...
written 5 weeks ago by
suzuBell • 40
• updated
5 weeks ago by
hafiz.talhamalik • 220
0
votes
0
answers
121
views
0
answers
... Thanks @gb. This is an example of what the beginning of the output of getORF looks like for me:
>NODE_43_length_251_cov_0.839080_1 [2 - 40]
tgcttgattgatagcataatagcggttattataagtggc
>NODE_43_length_251_cov_0.839080_2 [36 - 65]
gtggctagggggtcttgcaaattcaccgca
>NODE_43_len ...
written 6 weeks ago by
suzuBell • 40
0
votes
0
answers
121
views
0
answers
... Thanks @gb. I also tried the recommendation. My ordered contigs.fasta file has 1,500,360 bases. To determine ORFs, I first tried to use NCBI ORFFinder but it has a 50K limitation. Instead, I then tried getORF from EMBOSS. I used it on Galaxy platform with all the defaults. When I downloaded the resu ...
written 6 weeks ago by
suzuBell • 40
0
votes
0
answers
121
views
0
answers
... Thanks @gb. I'm in the process of trying your advice now. To make sure I clearly understand these points, I am trying to figure out three values for this bacterial genome 1) % coding, 2) Number of genes, 3) Number of protein coding genes. It sounds like %coding is just taking the total number of bas ...
written 6 weeks ago by
suzuBell • 40
0
votes
1
answer
105
views
1
answers
... Hi @yztxwd. Thanks for the comment. I tried changing the second line to both homp (my $uname = "Linux") and homp (my $uname = "IRIX64"). When I used "Linux", and ran the code `rnammer -S bac -m tsu,ssu,lsu -gff output_gff -h output_hmmreport -f output_fasta sample1.fasta` I do now get a output_gff f ...
written 6 weeks ago by
suzuBell • 40
0
votes
1
answer
105
views
1
answer
... I recently tried to user rnammer.
1. I first used the web browser version and uploaded a .fasta file. Unfortunately, this resulted in an error as my .fasta file contains more than 1,000,000 total residues (twice as much in fact).
2. I decided to try the command line version to see if it could acce ...
2
votes
0
answers
121
views
0
answers
... Reading a paper with interesting statistics on bacterial genomes ([here][1]). It states that "The average protein coding content of a bacterial genome is 88% for the 2671 finished genomes in GenBank".
I have assembled the contigs of a bacterial genome and have a contigs.fasta file. Is there a quic ...
written 7 weeks ago by
suzuBell • 40
Latest awards to suzuBell
Student
5 weeks ago,
asked a question with at least 3 up-votes.
For Determine number and length of plasmids in bacterial genome (using something like Prokka)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1743 users visited in the last hour