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Author Topic:   Sequence comparisons (Bioinformatics?)
Entomologista
Inactive Member


Message 16 of 42 (216048)
06-11-2005 12:13 AM
Reply to: Message 1 by NosyNed
06-08-2005 6:45 PM


Personally, I like the program Biology Workbench. http://workbench.sdsc.edu/
"Note also that prior to the molecular data, there were anatomists that speculated"
You don't want to start the morphological vs molecular data debate. You'll never hear the end of it from the morphologists. Trust me.

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randman 
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Posts: 6367
Joined: 05-26-2005


Message 17 of 42 (216062)
06-11-2005 2:26 AM
Reply to: Message 16 by Entomologista
06-11-2005 12:13 AM


Turtle, Kangaroo, and Rattlesnake
This is what I got for CytoC comparisons for turtle, kangaroo and rattlesnake.
{qs Sequence 1: TurtleCytC>GDVEKGKKIFVQKCAQCHT 34 aa
Sequence 2: KangarooCytC>GDVEKGKKIFVQKCAQC 34 aa
Sequence 3: RattlesnaleCytC>GDVEKGKKIFSMKC 34 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 88.2353
Sequences (1:3) Aligned. Score: 76.4706
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 73.5294
Sequences (3:2) Aligned. Score: 73.5294
Sequences (3:3) Aligned. Score: 100 [/qs]
This suggests that the kangaroo and the turtle are more closely related than the turtle and rattlesnake, but that's not what current phylogenies would predict.

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randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 18 of 42 (216063)
06-11-2005 2:40 AM
Reply to: Message 17 by randman
06-11-2005 2:26 AM


Re: Turtle, Kangaroo, and Rattlesnake
Also, with humans added. People are more related to rattlesnakes than kangaroos.....hmmm.
Sequence 1: TurtleCytC>GDVEKGKKIFVQKCAQCHT 34 aa
Sequence 2: KangarooCytC>GDVEKGKKIFVQKCAQC 34 aa
Sequence 3: RattlesnaleCytC>GDVEKGKKIFSMKC 34 aa
Sequence 4: humancytoC>MPSTLPAPRRTHAARTASL 378 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 88.2353
Sequences (1:3) Aligned. Score: 76.4706
Sequences (1:4) Aligned. Score: 20.5882
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 73.5294
Sequences (2:4) Aligned. Score: 17.6471
Sequences (3:2) Aligned. Score: 73.5294
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 23.5294
Sequences (4:2) Aligned. Score: 17.6471
Sequences (4:3) Aligned. Score: 23.5294
Sequences (4:4) Aligned. Score: 100
This message has been edited by randman, 06-11-2005 02:41 AM

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randman 
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Posts: 6367
Joined: 05-26-2005


Message 19 of 42 (216064)
06-11-2005 2:48 AM


here's one with CytoB
It still doesn't match with current hypotheses.
It looks like the site will give you wrong data for common names. I looked up and ran the scientific names though, and got the following. Please note that "alligator" is alligator snapping turtle, aka Macroclemys temminckii.
Sequence 1: humanCytoB>MTPMRKINPLMKLINHSFI 308 aa
Sequence 2: rattlesnakeCytoB>MMQTMTGFFLAIH 155 aa
Sequence 3: redkangaroo>MTNLRKTHPLIKIVNHSF 311 aa
Sequence 4: alligator 198 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 58.7097
Sequences (1:3) Aligned. Score: 75.6494
Sequences (1:4) Aligned. Score: 77.7778
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 61.2903
Sequences (2:4) Aligned. Score: 62.5806
Sequences (3:2) Aligned. Score: 61.2903
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 77.2727
Sequences (4:2) Aligned. Score: 62.5806
Sequences (4:3) Aligned. Score: 77.2727
Sequences (4:4) Aligned. Score: 100

>humanCytoB>MTPMRKINPLMKLINHSFIDLPTPSNISAWWNF
GSLLGACLILQITTGLFLAMHYSPDASTAFSSIAHIT
RDVNYGWIIRYLHANGASMFFICLFLHIGRGLYYGSFL
YSETWNIGIILLLATMATAFMGYVLPWGQMSF
WGATVITNLLSAIPYIGTDLVQWIWGGYSVDSPTLTRFF
TFHFILPFIIAALAALHLLFLHETGSNNPLG
ITSHSDKITFHPYYTIKDALGLLLFLLSLMTLTLFSPDLLGDPDN
YTLANPLNTPPHIKPEWYFLFAYTI
LRSVPNKLGGVLALLLSILILAMIPILHMSKQQSMMF
RPLSQSLYWLLAADLLILTWIGGQPVSYPFTII
GQVASVLYFTTILILMPTISLIENKMLK
>rattlesnakeCytoB>MMQTMTGFFLAIHYTANINLAFSSVIHITRDVPYGXIMQNLHTISASL
FFICIYIHIARGLYYGLYLNKE
VWLSGTALLITLMATAFFGYVLPWGQMSFWAATVITNLLTAIPYLGTTLTTWL
WGGFSINDPTLTRFFAL
HFILPFIIISLSSIHIILLHNEGSNNPLGTNSDIDKIPFHPYHS
YKDVLMITSMITLLLLILSFSPSLLN
DPENFXKAXPXXTPQ
>redkangaroo>MTNLRKTHPLIKIVNHSFIDLPAPSNISAWWNF
GSLLGACLIIQILTGLFLAMHYTADTLTAFSSVAHIC
RDVNYGWLIRNLHANGASMFFMCLFLHVGRGIYYGSYLYKETW
NIGVILLLTVMATAFVGYVLPWGQMSF
WGATVITNLLSAIPYIGTTLVEWIWGGFSVDKATLTRFFAFHF
ILPFIITALVLVHLLFLHETGSNNPSG
INPDSDKIPFHPYYTIKDALGFMLMLLILLTLALFSPDML
GDPDNFSPAKPTEHSSHIKPEWYFLFAYAI
LRSIPNKLGGVLALLASILILLIIPLLHTSKQRSLMFRPISQTLF
WILTANLITLTWIGGQPVEQPYIII
GQVASISYFLLIIVLMPLAGLFENYMLEPKW
>alligator snapping turlte>MATNLRKTHPMMKIINNSFIDLPSPSNISAWWNFGSLLGTCLI
MQTITGIFLAMHYSPDISMAFSSITHI
TRDVQYGWLIRNMHANGASLFFICIYLHIGRGLYYGSYL
YKETWNTGVILLLLTMATAFMGYVLPWGQMS
FWGATVITNLLSAIPYIGSTLVQWIWGGFSVDNATLTRFFTLHFLLPFTIMG
LAMVHLLFLHETGSNNPT
GLNSNSDKIPFHPYFSYKDLLGLILMLSLLLTLALFSPNLLGDPDNFTPANPLVTPPH
Humans are more related to alligator snapping turtles than a red kangaroo, aka Macropus rufus?
This message has been edited by randman, 06-11-2005 03:28 AM
This message has been edited by AdminJar, 06-12-2005 10:56 AM

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randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 20 of 42 (216080)
06-11-2005 4:02 AM


Cyto B comparisons for a mouse, human, red wolf, and alligator snapping turtle.
Sequence 1: MusmusculusCytoB>MGDWAVNEGLSIF 500 aa
Sequence 2: humanCytoB>MTPMRKINPLMKLINHSFI 308 aa
Sequence 3: MacropusrufusCytB>MTNLRKTHPLIK 311 aa
Sequence 4: Macroclemys 198 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 11.039
Sequences (1:3) Aligned. Score: 11.8971
Sequences (1:4) Aligned. Score: 12.1212
Sequences (2:2) Aligned. Score: 100
Sequences (2:3) Aligned. Score: 75.6494
Sequences (2:4) Aligned. Score: 77.7778
Sequences (3:2) Aligned. Score: 75.6494
Sequences (3:3) Aligned. Score: 100
Sequences (3:4) Aligned. Score: 77.2727
Sequences (4:2) Aligned. Score: 77.7778
Sequences (4:3) Aligned. Score: 77.2727
Sequences (4:4) Aligned. Score: 100

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 21 of 42 (216090)
06-11-2005 5:03 AM
Reply to: Message 19 by randman
06-11-2005 2:48 AM


Re: here's one with CytoB
OK, lets have a look:
Crotalus molossus nigrescens (rattle snake)
Macropus rufus (Red Kangaroo)
Homo sapien
Alligator mississippiensis(Mississipi Aligator)
Macroclemys temminckii (alligator snapping turtle)
Hylomyscus alleni (Woodmouse)
Vombatus ursinus (Common Wombat)
Chelydra serpentina (Snapping turtle)
Crocodylus acutus (Crocodile)
That's one heck of a list there. Now when we run that we get:
quote:
Sequence 1: RedKangaroo 381 aa
Sequence 2: RattleSnake 225 aa
Sequence 3: Human 378 aa
Sequence 4: Alligator 386 aa
Sequence 5: SnappingTurtle 85 aa
Sequence 6: Woodmouse 380 aa
Sequence 7: Wombat 381 aa
Sequence 8: Crocodile 85 aa
Sequence 9: Snapping 297 aa
Sequences (4:5) Aligned. Score: 68Sequences (7:8) Aligned. Score: 67
Sequences (5:6) Aligned. Score: 74
Sequences (5:7) Aligned. Score: 76
Sequences (5:8) Aligned. Score: 69
Sequences (2:3) Aligned. Score: 59
Sequences (1:2) Aligned. Score: 60
Sequences (5:9) Aligned. Score: 96
Sequences (8:9) Aligned. Score: 69
Sequences (7:9) Aligned. Score: 78
Sequences (2:4) Aligned. Score: 53
Sequences (2:5) Aligned. Score: 69
Sequences (3:4) Aligned. Score: 64
Sequences (4:6) Aligned. Score: 63
Sequences (3:5) Aligned. Score: 82
Sequences (2:6) Aligned. Score: 61
Sequences (1:3) Aligned. Score: 75
Sequences (2:7) Aligned. Score: 61
Sequences (2:8) Aligned. Score: 56
Sequences (4:7) Aligned. Score: 67
Sequences (3:6) Aligned. Score: 76
Sequences (4:8) Aligned. Score: 78
Sequences (2:9) Aligned. Score: 64
Sequences (1:4) Aligned. Score: 66
Sequences (1:5) Aligned. Score: 76
Sequences (6:7) Aligned. Score: 80
Sequences (4:9) Aligned. Score: 69
Sequences (6:8) Aligned. Score: 65
Sequences (3:7) Aligned. Score: 75
Sequences (3:8) Aligned. Score: 67
Sequences (1:6) Aligned. Score: 81
Sequences (6:9) Aligned. Score: 77
Sequences (3:9) Aligned. Score: 77
Sequences (1:7) Aligned. Score: 88
Sequences (1:8) Aligned. Score: 69
Sequences (1:9) Aligned. Score: 77
Humans are more related to alligator snapping turtles than a red kangaroo, aka Macropus rufus?
Human/Alligator: Sequences (3:4) Aligned. Score: 64
Human/Kangaroo: Sequences (1:3) Aligned. Score: 75
Human/Snapping Turtle: Sequences (1:5) Aligned. Score: 76
Well, the numbers certainly support what your saying. But wait, there's more, look at the N J Tree
It doesn't get it totally right, but we don't expect it to, it seems to have done rather well. Now, as has been said, comparing one protien can give some ideas, but not the full picture, and there is significant room for error. We should consider 100s of genes to be able to come to a more solid conclusion.
This message has been edited by Modulous, Sat, 11-June-2005 10:13 AM

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 22 of 42 (216095)
06-11-2005 5:30 AM
Reply to: Message 17 by randman
06-11-2005 2:26 AM


Re: Turtle, Kangaroo, and Rattlesnake
Please post the whole of the FASTA sequences, or at least provide sufficient information so that other people can get hold of the neccessary sequence data. In fact it might be a good idea if from now on people gave us the accession numbers of the sequences they run.
One major problem here is that Cytochrome C is not 34 amino acids in length.
I tried to run the same alignment using the following sequences
>Grey Kangaroo CytC
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLNGIFGRKTGQAPGFTYTDANKNKGIIWGEDTLMEYLEN
PKKYIPGTKMIFAGIKKKGERADLIAYLKKATNE
>Snapping Turtle CytC
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLNGLIGRKTGQAEGFSYTEANKNKGITWGEETLMEYLEN
PKKYIPGTKMIFAGIKKKAERADLIAYLKDATSK
>Rattlesnake Cytochrome C
GDVEKGKKIFSMKCGTCHTVEEGGKHKTGPNLHGLFGRKTGQAVGYSYTAANKNKGIIWGDDTLMEYLEN
PKKYIPGTKMVFTGLKSKKERTDLIAYLKEATAK
As you can see the CytC sequences are 104aa in length. The sequence accessions are P68517 for the rattlesnake, P00022 for the turtle and P00014 for the Kangaroo.
I'm not sure how you ended up with only 34 amino acids for each species, I'm not sure that you are using the FASTA format correctly. It looks as if you are losing all of the sequence which is in the first line of amino acids in my input data and only getting the last 34 amino acids.
That aside the results are in line with yours.
Sequence type explicitly set to Protein
Sequence format is Pearson
Sequence 1: Grey Kangaroo 104 aa
Sequence 2: Snapping turtle 104 aa
Sequence 3: Rattlesnake 104 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 89
Sequences (2:3) Aligned. Score: 79
Sequences (1:3) Aligned. Score: 79
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 23 of 42 (216096)
06-11-2005 5:34 AM
Reply to: Message 19 by randman
06-11-2005 2:48 AM


Re: here's one with CytoB
Here is the problem!
Youre FASTA formatting is all wrong.
The correct format is
>Name
Sequence
i.e.
>Grey Kangaroo Cytochrome C
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLNGIFGRKTGQAPGFTYTDANKNKGIIWGEDTLMEYLEN
PKKYIPGTKMIFAGIKKKGERADLIAYLKKATNE
You need a line break after the name and only one '>' right at the start of the name for each sequence.At the moment you are losing big chunks of sequence data.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 24 of 42 (216098)
06-11-2005 5:53 AM
Reply to: Message 21 by Modulous
06-11-2005 5:03 AM


Re: here's one with CytoB
It would be a very good idea to check out the source of the data in a case where there are severe discrepancies in the lengths of the proteins.
A lot of the sequences in genbank are only partial coding sequences. For instance your 85aa sequence for the snapping turtle is only a partial coding sequence. There is a fuller, though still not complete, CDS based vesion here.
This sort of partial data is bound to affect the quality of any analysis you perform. To check the source data for your amino acid sequence click on the hyperlink at the 'DBSOURCE' entry in the GenPept view.
TTFN,
WK

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Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 25 of 42 (216102)
06-11-2005 6:36 AM
Reply to: Message 24 by Wounded King
06-11-2005 5:53 AM


Re: here's one with CytoB
Yeah - thanks for that. I was trying to see if it said on the main form that the sequences were only partial or not, I couldn't conceive of cytB being so short, but I went with the data I had.
I'll look into redoing the test later, thanks again - its useful to have someone around who is more than a keen amateur

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Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 26 of 42 (216112)
06-11-2005 9:02 AM
Reply to: Message 19 by randman
06-11-2005 2:48 AM


Re: here's one with CytoB
I tried it again with DNA rather than amino acids:
Rattlesnake
Kangaroo
Human
Alligator Snapping Turtle
Alligator
Woodmouse
Wombat
Snapper Turtle
Here is the results I got:
quote:
Sequence type explicitly set to DNA
Sequence format is Pearson
Sequence 1: Rattlesnake 675 bp
Sequence 2: Kangaroo 1146 bp
Sequence 3: Human 1135 bp
Sequence 4: AligatorSnappingTurtle 804 bp
Sequence 5: Alligator 1159 bp
Sequence 6: Woodmouse 1143 bp
Sequence 7: Wombat 1146 bp
Sequence 8: SnapperTurtle 892 bp
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 66
Sequences (4:5) Aligned. Score: 68
Sequences (7:8) Aligned. Score: 72
Sequences (3:4) Aligned. Score: 74
Sequences (1:3) Aligned. Score: 64
Sequences (6:7) Aligned. Score: 74
Sequences (4:6) Aligned. Score: 74
Sequences (2:3) Aligned. Score: 76
Sequences (5:6) Aligned. Score: 67
Sequences (1:4) Aligned. Score: 66
Sequences (6:8) Aligned. Score: 73
Sequences (4:7) Aligned. Score: 72
Sequences (1:5) Aligned. Score: 63
Sequences (3:5) Aligned. Score: 67
Sequences (2:4) Aligned. Score: 73
Sequences (4:8) Aligned. Score: 78
Sequences (1:6) Aligned. Score: 66
Sequences (5:7) Aligned. Score: 67
Sequences (1:7) Aligned. Score: 66
Sequences (3:6) Aligned. Score: 72
Sequences (2:5) Aligned. Score: 68
Sequences (5:8) Aligned. Score: 68
Sequences (1:8) Aligned. Score: 66
Sequences (3:7) Aligned. Score: 73
Sequences (2:6) Aligned. Score: 77
Sequences (3:8) Aligned. Score: 72
Sequences (2:7) Aligned. Score: 81
Sequences (2:8) Aligned. Score: 73
So, harking back to your quote:
Humans are more related to alligator snapping turtles than a red kangaroo, aka Macropus rufus?
Humans to aligator snapping turtles:
Sequences (3:4) Aligned. Score: 74
Humans to kangaroo:
Sequences (2:3) Aligned. Score: 76
Once we look at the actual DNA sequences the effect seems to go away. Still - we are suffering from a lack of complete DNA sequences here, I discarded the crocodile due to small sample size. I predict that if we have the full DNA sequence for cytochrome b for Alligator Snapping Turtles, the results will show us to be closer to the kangaroo. That said, it is possible for the opposite to be true, but I predict that when further protiens are examined, the result will be shown to be an anomolous outlier.

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randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 27 of 42 (216220)
06-11-2005 5:24 PM
Reply to: Message 26 by Modulous
06-11-2005 9:02 AM


Re: here's one with CytoB
Modulous, I don't doubt we are making mistakes, as WK, pointed out, but it seems the data is getting fairly consistent in placing turtles way too close to us compared to kangaroos, another mammal.
74 and 76 are nearly identical in some respects.
I have to be honest and state I chose the turtle, rattlesnake, humans, and kangaroo because I read somewhere the data did not fit. I am probably not even a "keen amatuer" when it comes to DNA, but the creationist that made that comment was correct, it seems.
Not sure what this means just yet though. I suspect we will have a better picture in a few years.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 28 of 42 (216370)
06-12-2005 9:06 AM


XP compatible version of ClustalX
This is for Mark24 since the other thread in which we were doing sequence analysis has been closed.
There is a windows version of ClustalX which should be compatible with XP, here. It comes bundled with the NJ-plot program as well, which you could use instead of Treeview.
TTFN,
WK
This message has been edited by Wounded King, 06-12-2005 09:07 AM

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mark24
Member (Idle past 5195 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 29 of 42 (216381)
06-12-2005 9:40 AM
Reply to: Message 28 by Wounded King
06-12-2005 9:06 AM


Re: XP compatible version of ClustalX
WK,
Yep, thank seems to run, I'll take a look later.
Thanks again,
Mark

There are 10 kinds of people in this world; those that understand binary, & those that don't

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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 30 of 42 (216383)
06-12-2005 9:54 AM
Reply to: Message 27 by randman
06-11-2005 5:24 PM


Nearly?
74 and 76 are nearly identical in some respects.
What are those respects? What does having similar percentages mean? What is "too close"? What is not close enough?
Are these not all relative numbers to position animals relative to each other?
There are some proteins that are identical across a wide range of animals are there not? If we picked those would a series of 100's result? Would that matter or be meaningful? In what way?
(I'm not called NOSY for nuttin' you know. )

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