Special:Log/restrict

Seddon — Fri, 20 Nov 2009 18:40:57 GMT

restricted Expression Data Notes

Expression Data Notes

Seddon — Fri, 20 Nov 2009 18:40:52 GMT

New page: hyfhyfhfy

New page

hyfhyfhfy

User:Seddon

Seddon — Fri, 20 Nov 2009 18:40:40 GMT

←Older revision		Revision as of 18:40, 20 November 2009
Line 1:		Line 1:
-	[[Image:~~IMG_4594~~.JPG\|frame\|left\|200x200px]]	+	[[Expression Data Notes]]
		+
		+
		+
		+
		+	[[Image:IMG 4594.JPG\|frame\|left\|200x200px]]

Special:Log/restrict

Moghe — Fri, 20 Nov 2009 18:39:45 GMT

restricted Project sORF

Project sORF

Shiu — Fri, 20 Nov 2009 15:24:30 GMT

New page

== Ortholog evol rate ==

*Working dir:
**/home/shiu/project/arabi_interg_expr/4_sORF_at_al/2_jgi_al_assembly/2_remap/1_at_sorf_vs_al_chr

=== Data parsing for Gaurav's ortholog ID procedures ===
*First search At sORF against Al genome assembly. With BlastUtility, example line:
/home/shiu/bin/blast//blastall -p tblastn -e 1 -F F -v 0 -b 2000 -i at_coding_orf_7442.fa_F0.trans_10 -o 10.out -d araly1_assm
#Parse the BLAST output to a format Gaurav can use:
cat *.out > at_sorf_vs_al_assm
# use ParseBlast.parse_align2 to get m=8 format
python ~/project/arabi_interg_expr/_script/script_4.2.2.1_for_gaurav.py at_sorf_vs_al_assm.mod

*Gaurav added At and Al annotations into the file. But need to be sorted based on Chr, left and right coordinates
ln -s /home/moghe/projects/9_RNAgenes_hopefullyfinal/1_try_lateSEP09/19_proteinbased_synteny/5_shinhan_coordinates/at_sorf_vs_al_assm.mod.gaurav.allpep
python ~/project/arabi_interg_expr/_script/script_4.2.2.1_sort.py at_sorf_vs_al_assm.mod.gaurav.allpep

=== Coding sequence identification using the pseudogene pipeline ===

*Process Gaurav ortholog data

#Parse ortholog assignment file from Gaurav
python ../../../../_script/script_4.2.2.1_parse_ortho_file.py
#Get lyrata orthologous region DNA sequences
python ~/codes/FastaManager.py -f get_stretch4 -fasta araly1_assm -coords al_ortho_at_sorf.coord

*Use part of the [[Plant pseudogenes|pseudogene pipeline]]

# SW alignments between at_sorf and al_ortho
python ~/codes/BlastUtility.py -f batch_sw -p tfasty -g at_sorf_vs_al_assm.ortho -i at_coding_orf_7442.fa_F0.trans -j al_ortho_at_sorf.coord.fa -bdir ~/bin/fasta3/ -d 1
Program  : tfasty34
Pair list: at_sorf_vs_al_assm.ortho
Fasta1  : at_coding_orf_7442.fa_F0.trans
Fasta2  : al_ortho_at_sorf.coord.fa
Fasta dir: /home/shiu/bin/fasta3/
Working d:
Flags  : -A -m 3 -q
E thres  : 1.0
Read gene pairs...
4328 pairs
# 4 pairs don't have proper SW alignments. Discarded
['AT_1|+|2|25914789-25914944', 'scaffold_2|13459371-13459415']
['AT_3|+|2|4263738-4263875', 'scaffold_3|5340338-5340379']
['AT_4|-|1|15993618-15993740', 'scaffold_7|3372795-3372830']
['AT_5|+|2|25818540-25818677', 'scaffold_8|21536704-21536751']
# Generate .disable_count file, defining what kinds of disablement are in the lyrata sequence
python ~/codes/_misc/pseudo/script_step6.py blosum50.matrix at_sorf_vs_al_assm.ortho.sw.out

*Many of the lyrata matches are really sort, and appear repetitive. See example below. Even though there is no obvious disablement, it is still not a good match. In these cases, need to find out how annotated genes are conserved between At and Al length-wise.

#AT_2|-|1|887310-887600 scaffold_5|1592334-1592375 79-92:1-42 3.1e-06 0 0 0 0
IYIYIYIYIYIHIY
LYIYIYIYIYIYIY

*Get the CDS out

# Parse .disable_count to generate a summary table and a coord file for subject matching area
ln -s at_sorf_vs_al_assm.ortho.sw.out.disable_count at_sorf_vs_al_assm.ortho.DC
python ~/codes/_misc/pseudo/script_step6_getcoord.py at_sorf_vs_al_assm.ortho.DC
# Get the lyrata sequences in SW aligned regions
python ~/codes/FastaManager.py -f get_stretch4 -fasta al_ortho_at_sorf.coord.fa -coords at_sorf_vs_al_assm.ortho.DC.subj_coord
# Start matching the SW alignments with nucleotide sequences
python ~/codes/_misc/pseudo/script_step7.py at_sorf_vs_al_assm.ortho.DC.subj_coord.fa at_sorf_vs_al_assm.ortho.DC > step7.log
# Rid of disabling mutations and translate the sequences.
python ~/codes/_misc/pseudo/script_step7.1.py at_sorf_vs_al_assm.ortho.DC.ps_cds
python ~/codes/Translation.py -f tl -cds at_sorf_vs_al_assm.ortho.DC.ps_cds.rid_allstop
Total 4250 sequences translated.
0 has length not divisable by 3.
0 has inner stop codon(s).
0 has unknown codons.

=== Rate calculation ===
# Consolidate sequences
cat at_coding_orf_7442.fa at_sorf_vs_al_assm.ortho.DC.ps_cds.rid_allstop > at_al_ps_cds
cat at_coding_orf_7442.fa_F0.trans at_sorf_vs_al_assm.ortho.DC.ps_cds.rid_allstop_F0.trans > at_al_ps_pep
# original names too long for clustal. Rename sequences
python ~/codes/FastaManager.py -f rename -fasta at_al_ps_cds -name at_al_new_names
python ~/codes/FastaManager.py -f rename -fasta at_al_ps_pep -name at_al_new_names
Fasta: 11692 entries, 8754 with new name
Name : 8754 entries, 7428 unique, 0 not in fasta
python ~/codes/AlnUtility.py -f rate_pair -nt at_al_ps_cds_rename.fa -pep at_al_ps_pep_rename.fa -paml ~/bin/paml4/bin/ -clustal ~/bin/ -pairs at_sorf_vs_al_assm.ortho.DC.pairs.new_names

* Results consolidated in at_sorf_al_ortho_align_disable_rate.xls

User:Li

Moghe — Wed, 18 Nov 2009 18:00:57 GMT

←Older revision		Revision as of 18:00, 18 November 2009
Line 1:		Line 1:
-	~~hjhjhjh[[Image:Earth.png]]~~	+	=Personal Information=
		+
		+	=Academic interests=
		+
		+	=Hobbies and other interests=

User:Li

Li — Wed, 18 Nov 2009 16:19:25 GMT

New page: hjhjhjhImage:Earth.png

New page

hjhjhjh[[Image:Earth.png]]

Special:Log/rights

Moghe — Wed, 18 Nov 2009 16:16:09 GMT

changed group membership for User:Li from viewrestrict to viewrestrict, restrict

Special:Log/rights

Moghe — Wed, 18 Nov 2009 16:16:06 GMT

changed group membership for User:Li from (none) to viewrestrict

People

Moghe — Wed, 18 Nov 2009 16:15:37 GMT

←Older revision		Revision as of 16:15, 18 November 2009
Line 143:		Line 143:

	{\| cellspacing="0" cellpadding="5" style="width: 90%;" class="FCK__ShowTableBorders"		{\| cellspacing="0" cellpadding="5" style="width: 90%;" class="FCK__ShowTableBorders"
-	\|-	+	\|- style="background: rgb(176, 224, 230) none repeat scroll 0% 50%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"
-	\|	+	\| {{Click \|
		+	\| image = Earth.png
		+	\| link = User:Li
		+	\| width = 60px
		+	\| height=60px
		+	}}
		+	\| [[User:Li\|Jiying Li]]
		+	\| '''Rotating graduate student'''
		+	BS, China Agricultural University, Beijing
		+
	\|}		\|}

Shiu Lab - Recent changes [en]

Special:Log/restrict

Expression Data Notes

User:Seddon

Special:Log/restrict

Project sORF

User:Li

User:Li

Special:Log/rights

Special:Log/rights

People