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# System prepended metadata

title: Lab 4

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# Lab 4
`grep tssB /courses/bi278/Course_Materials/lab_04/PROKKA*.tsv`
Used this to get to file rather than suggested 'grep tssB bhqs69/PROKKA*.tsv'
I ruined everything
Had to restart and 'cp /courses/bi278/Course_Materials/lab_04/bhqs69/PROKKA_09242022.tsv lab_04'
then mkdir lab_04
then I could 'grep tssB lab_04/PROKKA*.tsv'
need to index the fasta file so that you can find individual genes within it
using a new software named samtools. Used 'samtools faidx lab_04/PROKKA*.faa'
'samtools faidx lab_04/PROKKA*.faa BH69_01414 BH69_02561 BH69_03639' to view amino acid sequence
Didn't have bh69_tssB.faa in lab_04 so used 'mv bh69_tssB.faa lab_04' to get it in there
then got into directory with cd lab_04
then finally ran command 'cat t6ss_db.faa bh69_tssB.faa > tssB_input.faa' --> to link this file to the ones from T6SS
'muscle -align tssB_input.faa -output tssB_muscle.afa' aligned sequences
reordered using 'python stable_py3.py tssB_input.faa tssB_muscle.afa | grep ">"| head'
Now let’s fix the order and save it as a new file using 'python stable_py3.py tssB_input.faa tssB_muscle.afa > tssB_muscle.faa'
Basic alignment 'mafft --maxiterate 3 tssB_input.faa > tssB_mafft.faa'
The two alignments appear to have gaps in similar places. The order of the amino acid sequence seems, by and large, the same. I believe these similar regions represent conserved genes between species. They probably code for proteins that are present/functional in many organisms.
Q2: There is a gap in the MUSCLE sequence in the beginning vs. none in the MAFFT. I think this is due to a large 10 AA shift to the left from mafft. There is a large length difference between the two that may also be attributed to this. It seems like the start of the MUSCLE sequence is all squished together at the start of the mafft sequence. There's also a large gap at the end of the MUSCLE sequence and less of a gap at the end of the MAFFT sequence.
![](https://i.imgur.com/RSHBA9e.png)
![](https://i.imgur.com/z45tuVn.png)
Fire trees, huh?
